diff --git a/articles/Comparing2Groups.html b/articles/Comparing2Groups.html index 9398e4625..38006309f 100644 --- a/articles/Comparing2Groups.html +++ b/articles/Comparing2Groups.html @@ -102,8 +102,8 @@ - - + +
@@ -111,7 +111,7 @@

Comparing Two Groups with prolfqua

Witold E. Wolski

-

2024-01-23

+

2024-03-20

Source: vignettes/Comparing2Groups.Rmd @@ -528,8 +528,8 @@

Compute contrasts
 plotter$ma_plotly()

-
-

+

+

MA plot showing the dependency of mean abuncance with respect to the difference

@@ -596,9 +596,9 @@

GSEA Analyis
 #evalAll <- require("clusterProfiler") & require("org.Sc.sgd.db") & require("prora")
-evalAll <- require("clusterProfiler") & require("org.Sc.sgd.db2") & require("prora")

+evalAll <- require("clusterProfiler") & require("org.Sc.sgd.db2") & require("prora")
-library(clusterProfiler)
+library(clusterProfiler)
 library(org.Sc.sgd.db)
 
 bb <- prolfqua::get_UniprotID_from_fasta_header(merged$merged$get_contrasts(),
@@ -606,16 +606,16 @@ 
GSEA Analyisbb <- prora::map_ids_uniprot(bb)
 ranklist <- bb$statistic
 names(ranklist) <- bb$P_ENTREZGENEID
-res <- clusterProfiler::gseGO(
+res <- clusterProfiler::gseGO(
   sort(ranklist, decreasing = TRUE),
   OrgDb = org.Sc.sgd.db,
   ont = "ALL")
-ridgeplot( res )
+ridgeplot( res )
-dotplot(res , showCategory = 30)
+dotplot(res , showCategory = 30) 
-enrichplot::upsetplot(res)
+enrichplot::upsetplot(res)

The prolfqua package is described in (Wolski et al. 2022).

@@ -641,29 +641,56 @@

Session Info## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: -## [1] prolfqua_1.1.5 +## [1] clusterProfiler_4.8.2 prolfqua_1.1.5 ## ## loaded via a namespace (and not attached): -## [1] gtable_0.3.4 xfun_0.40 bslib_0.5.1 ggplot2_3.4.4 -## [5] htmlwidgets_1.6.2 ggrepel_0.9.3 crosstalk_1.2.0 vctrs_0.6.4 -## [9] tools_4.3.2 generics_0.1.3 tibble_3.2.1 fansi_1.0.5 -## [13] pkgconfig_2.0.3 KernSmooth_2.23-22 pheatmap_1.0.12 data.table_1.14.8 -## [17] RColorBrewer_1.1-3 desc_1.4.2 readxl_1.4.2 lifecycle_1.0.3 -## [21] compiler_4.3.2 farver_2.1.1 stringr_1.5.0 progress_1.2.2 -## [25] textshaping_0.3.6 munsell_0.5.0 httpuv_1.6.11 htmltools_0.5.6 -## [29] sass_0.4.7 yaml_2.3.7 lazyeval_0.2.2 plotly_4.10.1 -## [33] later_1.3.1 crayon_1.5.2 pillar_1.9.0 pkgdown_2.0.7 -## [37] jquerylib_0.1.4 tidyr_1.3.0 ellipsis_0.3.2 MASS_7.3-60 -## [41] cachem_1.0.8 mime_0.12 tidyselect_1.2.0 conflicted_1.2.0 -## [45] digest_0.6.33 stringi_1.7.12 dplyr_1.1.3 purrr_1.0.2 -## [49] labeling_0.4.3 forcats_1.0.0 rprojroot_2.0.3 fastmap_1.1.1 -## [53] grid_4.3.2 colorspace_2.1-0 cli_3.6.1 magrittr_2.0.3 -## [57] utf8_1.2.3 withr_2.5.1 promises_1.2.1 prettyunits_1.1.1 -## [61] scales_1.2.1 rmarkdown_2.25 httr_1.4.7 gridExtra_2.3 -## [65] cellranger_1.1.0 hms_1.1.3 ragg_1.2.5 shiny_1.7.5 -## [69] memoise_2.0.1 evaluate_0.21 knitr_1.44 viridisLite_0.4.2 -## [73] rlang_1.1.1 Rcpp_1.0.11 xtable_1.8-4 glue_1.6.2 -## [77] jsonlite_1.8.7 R6_2.5.1 systemfonts_1.0.4 fs_1.6.3 +## [1] RColorBrewer_1.1-3 jsonlite_1.8.8 magrittr_2.0.3 +## [4] farver_2.1.1 rmarkdown_2.26 fs_1.6.3 +## [7] zlibbioc_1.46.0 ragg_1.2.7 vctrs_0.6.5 +## [10] memoise_2.0.1 RCurl_1.98-1.14 ggtree_3.8.2 +## [13] htmltools_0.5.7 forcats_1.0.0 progress_1.2.3 +## [16] cellranger_1.1.0 gridGraphics_0.5-1 sass_0.4.8 +## [19] KernSmooth_2.23-22 bslib_0.6.1 htmlwidgets_1.6.4 +## [22] desc_1.4.3 plyr_1.8.9 plotly_4.10.4 +## [25] cachem_1.0.8 conflicted_1.2.0 igraph_2.0.2 +## [28] mime_0.12 lifecycle_1.0.4 pkgconfig_2.0.3 +## [31] gson_0.1.0 Matrix_1.6-5 R6_2.5.1 +## [34] fastmap_1.1.1 GenomeInfoDbData_1.2.10 shiny_1.8.0 +## [37] aplot_0.2.2 digest_0.6.34 enrichplot_1.20.0 +## [40] colorspace_2.1-0 patchwork_1.2.0 AnnotationDbi_1.62.2 +## [43] S4Vectors_0.38.2 textshaping_0.3.7 crosstalk_1.2.1 +## [46] RSQLite_2.3.5 labeling_0.4.3 fansi_1.0.6 +## [49] polyclip_1.10-6 httr_1.4.7 compiler_4.3.2 +## [52] bit64_4.0.5 withr_3.0.0 downloader_0.4 +## [55] BiocParallel_1.34.2 viridis_0.6.5 DBI_1.2.2 +## [58] highr_0.10 ggforce_0.4.2 MASS_7.3-60.0.1 +## [61] HDO.db_0.99.1 tools_4.3.2 scatterpie_0.2.1 +## [64] ape_5.7-1 httpuv_1.6.14 glue_1.7.0 +## [67] nlme_3.1-164 GOSemSim_2.26.1 promises_1.2.1 +## [70] shadowtext_0.1.3 grid_4.3.2 reshape2_1.4.4 +## [73] fgsea_1.26.0 generics_0.1.3 gtable_0.3.4 +## [76] tidyr_1.3.1 data.table_1.15.2 hms_1.1.3 +## [79] tidygraph_1.3.1 utf8_1.2.4 XVector_0.40.0 +## [82] BiocGenerics_0.46.0 ggrepel_0.9.5 pillar_1.9.0 +## [85] stringr_1.5.1 yulab.utils_0.1.4 later_1.3.2 +## [88] splines_4.3.2 tweenr_2.0.3 dplyr_1.1.4 +## [91] treeio_1.24.3 lattice_0.22-5 bit_4.0.5 +## [94] tidyselect_1.2.0 GO.db_3.17.0 Biostrings_2.68.1 +## [97] knitr_1.45 gridExtra_2.3 IRanges_2.34.1 +## [100] stats4_4.3.2 xfun_0.42 graphlayouts_1.1.1 +## [103] Biobase_2.60.0 pheatmap_1.0.12 stringi_1.8.3 +## [106] ggfun_0.1.4 lazyeval_0.2.2 yaml_2.3.8 +## [109] evaluate_0.23 codetools_0.2-19 ggraph_2.2.1 +## [112] tibble_3.2.1 qvalue_2.32.0 ggplotify_0.1.2 +## [115] cli_3.6.2 xtable_1.8-4 systemfonts_1.0.6 +## [118] munsell_0.5.0 jquerylib_0.1.4 Rcpp_1.0.12 +## [121] GenomeInfoDb_1.36.4 readxl_1.4.3 png_0.1-8 +## [124] parallel_4.3.2 ellipsis_0.3.2 pkgdown_2.0.7 +## [127] ggplot2_3.5.0 blob_1.2.4 prettyunits_1.2.0 +## [130] DOSE_3.26.2 bitops_1.0-7 tidytree_0.4.6 +## [133] viridisLite_0.4.2 scales_1.3.0 purrr_1.0.2 +## [136] crayon_1.5.2 rlang_1.1.3 cowplot_1.1.3 +## [139] fastmatch_1.1-4 KEGGREST_1.40.1

References diff --git a/articles/Comparing2Groups_files/crosstalk-1.2.0/css/crosstalk.min.css b/articles/Comparing2Groups_files/crosstalk-1.2.1/css/crosstalk.min.css similarity index 100% rename from articles/Comparing2Groups_files/crosstalk-1.2.0/css/crosstalk.min.css rename to articles/Comparing2Groups_files/crosstalk-1.2.1/css/crosstalk.min.css diff --git a/articles/Comparing2Groups_files/crosstalk-1.2.0/js/crosstalk.js b/articles/Comparing2Groups_files/crosstalk-1.2.1/js/crosstalk.js similarity index 100% rename from articles/Comparing2Groups_files/crosstalk-1.2.0/js/crosstalk.js rename to articles/Comparing2Groups_files/crosstalk-1.2.1/js/crosstalk.js diff --git a/articles/Comparing2Groups_files/crosstalk-1.2.0/js/crosstalk.js.map b/articles/Comparing2Groups_files/crosstalk-1.2.1/js/crosstalk.js.map similarity index 100% rename from articles/Comparing2Groups_files/crosstalk-1.2.0/js/crosstalk.js.map rename to articles/Comparing2Groups_files/crosstalk-1.2.1/js/crosstalk.js.map diff --git a/articles/Comparing2Groups_files/crosstalk-1.2.0/js/crosstalk.min.js b/articles/Comparing2Groups_files/crosstalk-1.2.1/js/crosstalk.min.js similarity index 100% rename from articles/Comparing2Groups_files/crosstalk-1.2.0/js/crosstalk.min.js rename to articles/Comparing2Groups_files/crosstalk-1.2.1/js/crosstalk.min.js diff --git a/articles/Comparing2Groups_files/crosstalk-1.2.0/js/crosstalk.min.js.map b/articles/Comparing2Groups_files/crosstalk-1.2.1/js/crosstalk.min.js.map similarity index 100% rename from articles/Comparing2Groups_files/crosstalk-1.2.0/js/crosstalk.min.js.map rename to articles/Comparing2Groups_files/crosstalk-1.2.1/js/crosstalk.min.js.map diff --git a/articles/Comparing2Groups_files/crosstalk-1.2.0/scss/crosstalk.scss b/articles/Comparing2Groups_files/crosstalk-1.2.1/scss/crosstalk.scss similarity index 100% rename from articles/Comparing2Groups_files/crosstalk-1.2.0/scss/crosstalk.scss rename to 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b/articles/Comparing2Groups_files/figure-html/showIntensityDistributions-1.png index d55d4a156..ee33a6907 100644 Binary files a/articles/Comparing2Groups_files/figure-html/showIntensityDistributions-1.png and b/articles/Comparing2Groups_files/figure-html/showIntensityDistributions-1.png differ diff --git a/articles/Comparing2Groups_files/htmlwidgets-1.6.2/htmlwidgets.js b/articles/Comparing2Groups_files/htmlwidgets-1.6.4/htmlwidgets.js similarity index 100% rename from articles/Comparing2Groups_files/htmlwidgets-1.6.2/htmlwidgets.js rename to articles/Comparing2Groups_files/htmlwidgets-1.6.4/htmlwidgets.js diff --git a/articles/Comparing2Groups_files/plotly-binding-4.10.1/plotly.js b/articles/Comparing2Groups_files/plotly-binding-4.10.4/plotly.js similarity index 99% rename from articles/Comparing2Groups_files/plotly-binding-4.10.1/plotly.js rename to articles/Comparing2Groups_files/plotly-binding-4.10.4/plotly.js index 1155269d3..7a2a143b6 100644 --- a/articles/Comparing2Groups_files/plotly-binding-4.10.1/plotly.js +++ b/articles/Comparing2Groups_files/plotly-binding-4.10.4/plotly.js @@ -521,15 +521,17 @@ HTMLWidgets.widget({ // communication between the widget and direct manipulation events if (x.selectize) { var selectizeID = Object.keys(x.selectize)[i]; - var items = x.selectize[selectizeID].items; + var options = x.selectize[selectizeID]; var first = [{value: "", label: "(All)"}]; - var opts = { - options: first.concat(items), - searchField: "label", - valueField: "value", - labelField: "label", - maxItems: 50 - }; + var opts = $.extend({ + options: first.concat(options.items), + searchField: "label", + valueField: "value", + labelField: "label", + maxItems: 50 + }, + options + ); var select = $("#" + selectizeID).find("select")[0]; var selectize = $(select).selectize(opts)[0].selectize; // NOTE: this callback is triggered when *directly* altering diff --git a/articles/CreatingConfigurations.html b/articles/CreatingConfigurations.html index 829addc25..72ec65232 100644 --- a/articles/CreatingConfigurations.html +++ b/articles/CreatingConfigurations.html @@ -109,7 +109,7 @@

Creating prolfqua Configurations

Witold E. Wolski

-

2024-01-23

+

2024-03-20

Source: vignettes/CreatingConfigurations.Rmd @@ -296,25 +296,25 @@

Session Info## [1] stats graphics grDevices utils datasets methods base ## ## loaded via a namespace (and not attached): -## [1] gtable_0.3.4 xfun_0.40 bslib_0.5.1 ggplot2_3.4.4 -## [5] htmlwidgets_1.6.2 ggrepel_0.9.3 tzdb_0.4.0 vctrs_0.6.4 +## [1] gtable_0.3.4 xfun_0.42 bslib_0.6.1 ggplot2_3.5.0 +## [5] htmlwidgets_1.6.4 ggrepel_0.9.5 tzdb_0.4.0 vctrs_0.6.5 ## [9] tools_4.3.2 generics_0.1.3 parallel_4.3.2 tibble_3.2.1 -## [13] fansi_1.0.5 pkgconfig_2.0.3 pheatmap_1.0.12 data.table_1.14.8 -## [17] RColorBrewer_1.1-3 desc_1.4.2 lifecycle_1.0.3 prolfqua_1.1.5 -## [21] compiler_4.3.2 farver_2.1.1 stringr_1.5.0 textshaping_0.3.6 -## [25] munsell_0.5.0 htmltools_0.5.6 sass_0.4.7 yaml_2.3.7 -## [29] lazyeval_0.2.2 plotly_4.10.1 crayon_1.5.2 pillar_1.9.0 -## [33] pkgdown_2.0.7 jquerylib_0.1.4 tidyr_1.3.0 MASS_7.3-60 -## [37] cachem_1.0.8 tidyselect_1.2.0 conflicted_1.2.0 digest_0.6.33 -## [41] stringi_1.7.12 dplyr_1.1.3 purrr_1.0.2 labeling_0.4.3 -## [45] forcats_1.0.0 rprojroot_2.0.3 fastmap_1.1.1 grid_4.3.2 -## [49] archive_1.1.5 colorspace_2.1-0 cli_3.6.1 magrittr_2.0.3 -## [53] utf8_1.2.3 readr_2.1.4 withr_2.5.1 scales_1.2.1 -## [57] bit64_4.0.5 rmarkdown_2.25 httr_1.4.7 bit_4.0.5 -## [61] gridExtra_2.3 ragg_1.2.5 hms_1.1.3 memoise_2.0.1 -## [65] evaluate_0.21 knitr_1.44 viridisLite_0.4.2 rlang_1.1.1 -## [69] Rcpp_1.0.11 glue_1.6.2 vroom_1.6.3 jsonlite_1.8.7 -## [73] R6_2.5.1 systemfonts_1.0.4 fs_1.6.3 +## [13] fansi_1.0.6 highr_0.10 pkgconfig_2.0.3 pheatmap_1.0.12 +## [17] data.table_1.15.2 RColorBrewer_1.1-3 desc_1.4.3 lifecycle_1.0.4 +## [21] prolfqua_1.1.5 compiler_4.3.2 farver_2.1.1 stringr_1.5.1 +## [25] textshaping_0.3.7 munsell_0.5.0 htmltools_0.5.7 sass_0.4.8 +## [29] yaml_2.3.8 lazyeval_0.2.2 plotly_4.10.4 pillar_1.9.0 +## [33] pkgdown_2.0.7 crayon_1.5.2 jquerylib_0.1.4 tidyr_1.3.1 +## [37] MASS_7.3-60.0.1 cachem_1.0.8 tidyselect_1.2.0 conflicted_1.2.0 +## [41] digest_0.6.34 stringi_1.8.3 dplyr_1.1.4 purrr_1.0.2 +## [45] labeling_0.4.3 forcats_1.0.0 fastmap_1.1.1 grid_4.3.2 +## [49] archive_1.1.7 colorspace_2.1-0 cli_3.6.2 magrittr_2.0.3 +## [53] utf8_1.2.4 readr_2.1.5 withr_3.0.0 scales_1.3.0 +## [57] bit64_4.0.5 rmarkdown_2.26 httr_1.4.7 bit_4.0.5 +## [61] gridExtra_2.3 ragg_1.2.7 hms_1.1.3 memoise_2.0.1 +## [65] evaluate_0.23 knitr_1.45 viridisLite_0.4.2 rlang_1.1.3 +## [69] Rcpp_1.0.12 glue_1.7.0 vroom_1.6.5 jsonlite_1.8.8 +## [73] R6_2.5.1 systemfonts_1.0.6 fs_1.6.3

References diff --git a/articles/Modelling2Factors.html b/articles/Modelling2Factors.html index 631c38bd0..683b0ae67 100644 --- a/articles/Modelling2Factors.html +++ b/articles/Modelling2Factors.html @@ -109,7 +109,7 @@

Modelling dataset with two Factors

Witold E. Wolski

-

2024-01-23

+

2024-03-20

Source: vignettes/Modelling2Factors.Rmd @@ -355,26 +355,11 @@

Look at Proteins wi

Testing interaction computation

-
-url <- "https://raw.githubusercontent.com/genomicsclass/dagdata/master/inst/extdata/spider_wolff_gorb_2013.csv"
-filename <- "spider_wolff_gorb_2013.csv"
-downloader::download(url, filename)
-spider <- read.csv(filename, skip = 1)
-XA <- lm(friction ~ type * leg, data = spider)
-summary(XA)
-
-head(spider)
-spider <- spider |> tidyr::unite(legtype , leg, type, remove = FALSE)
-XF <- lm(friction ~ legtype - 1, data = spider)
-
-summary(glht(XF, linfct = rbind(i1 = c(1, -1, -1, 1 ,0, 0, 0, 0))))
-summary(glht(XF, linfct = rbind(i1 = c(1, -1, 0, 0, -1, 1, 0, 0 ))))
-summary(glht(XF, linfct = rbind(i1 = c(1, -1, 0, 0,  0, 0, -1, 1  ))))

Session Info

-
+
 
## R version 4.3.2 (2023-10-31)
 ## Platform: aarch64-apple-darwin20 (64-bit)
@@ -394,27 +379,27 @@ 
Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] beeswarm_0.4.0     gtable_0.3.4       xfun_0.40          bslib_0.5.1       
-##  [5] ggplot2_3.4.4      htmlwidgets_1.6.2  rstatix_0.7.2      ggrepel_0.9.3     
-##  [9] vctrs_0.6.4        tools_4.3.2        generics_0.1.3     tibble_3.2.1      
-## [13] fansi_1.0.5        pkgconfig_2.0.3    pheatmap_1.0.12    data.table_1.14.8 
-## [17] RColorBrewer_1.1-3 desc_1.4.2         lifecycle_1.0.3    prolfqua_1.1.5    
-## [21] farver_2.1.1       compiler_4.3.2     stringr_1.5.0      textshaping_0.3.6 
-## [25] progress_1.2.2     munsell_0.5.0      carData_3.0-5      vipor_0.4.5       
-## [29] htmltools_0.5.6    sass_0.4.7         yaml_2.3.7         lazyeval_0.2.2    
-## [33] plotly_4.10.1      car_3.1-2          ggpubr_0.6.0       pillar_1.9.0      
-## [37] pkgdown_2.0.7      crayon_1.5.2       jquerylib_0.1.4    tidyr_1.3.0       
-## [41] MASS_7.3-60        cachem_1.0.8       abind_1.4-5        tidyselect_1.2.0  
-## [45] conflicted_1.2.0   digest_0.6.33      stringi_1.7.12     dplyr_1.1.3       
-## [49] purrr_1.0.2        labeling_0.4.3     forcats_1.0.0      cowplot_1.1.1     
-## [53] rprojroot_2.0.3    fastmap_1.1.1      grid_4.3.2         colorspace_2.1-0  
-## [57] cli_3.6.1          magrittr_2.0.3     utf8_1.2.3         broom_1.0.4       
-## [61] withr_2.5.1        backports_1.4.1    prettyunits_1.1.1  scales_1.2.1      
-## [65] ggbeeswarm_0.7.2   rmarkdown_2.25     httr_1.4.7         gridExtra_2.3     
-## [69] ggsignif_0.6.4     ragg_1.2.5         hms_1.1.3          memoise_2.0.1     
-## [73] evaluate_0.21      knitr_1.44         viridisLite_0.4.2  rlang_1.1.1       
-## [77] Rcpp_1.0.11        glue_1.6.2         jsonlite_1.8.7     R6_2.5.1          
-## [81] systemfonts_1.0.4  fs_1.6.3

+##  [1] beeswarm_0.4.0     gtable_0.3.4       xfun_0.42          bslib_0.6.1       
+##  [5] ggplot2_3.5.0      htmlwidgets_1.6.4  rstatix_0.7.2      ggrepel_0.9.5     
+##  [9] vctrs_0.6.5        tools_4.3.2        generics_0.1.3     tibble_3.2.1      
+## [13] fansi_1.0.6        highr_0.10         pkgconfig_2.0.3    pheatmap_1.0.12   
+## [17] data.table_1.15.2  RColorBrewer_1.1-3 desc_1.4.3         lifecycle_1.0.4   
+## [21] prolfqua_1.1.5     compiler_4.3.2     farver_2.1.1       stringr_1.5.1     
+## [25] textshaping_0.3.7  progress_1.2.3     munsell_0.5.0      carData_3.0-5     
+## [29] vipor_0.4.7        htmltools_0.5.7    sass_0.4.8         yaml_2.3.8        
+## [33] lazyeval_0.2.2     plotly_4.10.4      car_3.1-2          pillar_1.9.0      
+## [37] pkgdown_2.0.7      ggpubr_0.6.0       crayon_1.5.2       jquerylib_0.1.4   
+## [41] tidyr_1.3.1        MASS_7.3-60.0.1    cachem_1.0.8       abind_1.4-5       
+## [45] tidyselect_1.2.0   conflicted_1.2.0   digest_0.6.34      stringi_1.8.3     
+## [49] dplyr_1.1.4        purrr_1.0.2        labeling_0.4.3     forcats_1.0.0     
+## [53] cowplot_1.1.3      fastmap_1.1.1      grid_4.3.2         colorspace_2.1-0  
+## [57] cli_3.6.2          magrittr_2.0.3     utf8_1.2.4         broom_1.0.5       
+## [61] withr_3.0.0        backports_1.4.1    prettyunits_1.2.0  scales_1.3.0      
+## [65] ggbeeswarm_0.7.2   rmarkdown_2.26     httr_1.4.7         gridExtra_2.3     
+## [69] ggsignif_0.6.4     ragg_1.2.7         hms_1.1.3          memoise_2.0.1     
+## [73] evaluate_0.23      knitr_1.45         viridisLite_0.4.2  rlang_1.1.3       
+## [77] Rcpp_1.0.12        glue_1.7.0         jsonlite_1.8.8     R6_2.5.1          
+## [81] systemfonts_1.0.6  fs_1.6.3

References diff --git a/articles/Modelling2Factors_files/figure-html/doGroupAverageImputation-1.png b/articles/Modelling2Factors_files/figure-html/doGroupAverageImputation-1.png index e063479f1..6229f0dd1 100644 Binary files a/articles/Modelling2Factors_files/figure-html/doGroupAverageImputation-1.png and b/articles/Modelling2Factors_files/figure-html/doGroupAverageImputation-1.png differ diff --git a/articles/Modelling2Factors_files/figure-html/prepareForGroupAverageImputation-2.png b/articles/Modelling2Factors_files/figure-html/prepareForGroupAverageImputation-2.png index 678fc5960..eed700a94 100644 Binary files a/articles/Modelling2Factors_files/figure-html/prepareForGroupAverageImputation-2.png and b/articles/Modelling2Factors_files/figure-html/prepareForGroupAverageImputation-2.png differ diff --git a/articles/Modelling2Factors_files/figure-html/unnamed-chunk-1-1.png b/articles/Modelling2Factors_files/figure-html/unnamed-chunk-1-1.png index 966fbb797..da0291cbe 100644 Binary files a/articles/Modelling2Factors_files/figure-html/unnamed-chunk-1-1.png and b/articles/Modelling2Factors_files/figure-html/unnamed-chunk-1-1.png differ diff --git a/articles/Modelling2Factors_files/figure-html/visualiseResults-1.png b/articles/Modelling2Factors_files/figure-html/visualiseResults-1.png index ec7d27670..a2129f24e 100644 Binary files a/articles/Modelling2Factors_files/figure-html/visualiseResults-1.png and b/articles/Modelling2Factors_files/figure-html/visualiseResults-1.png differ diff --git a/articles/Modelling2Factors_files/figure-html/visualiseResults-2.png b/articles/Modelling2Factors_files/figure-html/visualiseResults-2.png index 18acfde4d..b9df5b5ed 100644 Binary files a/articles/Modelling2Factors_files/figure-html/visualiseResults-2.png and b/articles/Modelling2Factors_files/figure-html/visualiseResults-2.png differ diff --git a/articles/QCandSampleSize.html b/articles/QCandSampleSize.html index 2cd223f0a..fbce90528 100644 --- a/articles/QCandSampleSize.html +++ b/articles/QCandSampleSize.html @@ -110,7 +110,7 @@

Quality Control & Sample Size

Witold Wolski

-

23 January, 2024

+

20 March, 2024

Source: vignettes/QCandSampleSize.Rmd diff --git a/articles/QCandSampleSize_files/figure-html/missingFigIntensityHistorgram-1.png b/articles/QCandSampleSize_files/figure-html/missingFigIntensityHistorgram-1.png index 17f983a4b..b3b719d6b 100644 Binary files a/articles/QCandSampleSize_files/figure-html/missingFigIntensityHistorgram-1.png and b/articles/QCandSampleSize_files/figure-html/missingFigIntensityHistorgram-1.png differ diff --git a/articles/QCandSampleSize_files/figure-html/pairsplotSmooth-1.png b/articles/QCandSampleSize_files/figure-html/pairsplotSmooth-1.png index f7e725778..6f6c87d6b 100644 Binary files a/articles/QCandSampleSize_files/figure-html/pairsplotSmooth-1.png and b/articles/QCandSampleSize_files/figure-html/pairsplotSmooth-1.png differ diff --git a/articles/QualityControlAndSampleSizeEstimation.html b/articles/QualityControlAndSampleSizeEstimation.html index c9fc3c703..4aa1ffa3f 100644 --- a/articles/QualityControlAndSampleSizeEstimation.html +++ b/articles/QualityControlAndSampleSizeEstimation.html @@ -109,7 +109,7 @@

QC and Sample Size Estimation

Witold E. Wolski

-

2024-01-23

+

2024-03-20

Source: vignettes/QualityControlAndSampleSizeEstimation.Rmd @@ -881,25 +881,25 @@

Session Info## [1] stats graphics grDevices utils datasets methods base ## ## loaded via a namespace (and not attached): -## [1] gtable_0.3.4 xfun_0.40 bslib_0.5.1 ggplot2_3.4.4 -## [5] htmlwidgets_1.6.2 ggrepel_0.9.3 lattice_0.21-9 vctrs_0.6.4 -## [9] tools_4.3.2 generics_0.1.3 tibble_3.2.1 fansi_1.0.5 -## [13] pkgconfig_2.0.3 KernSmooth_2.23-22 Matrix_1.6-1.1 pheatmap_1.0.12 -## [17] data.table_1.14.8 RColorBrewer_1.1-3 desc_1.4.2 readxl_1.4.2 -## [21] lifecycle_1.0.3 prolfqua_1.1.5 compiler_4.3.2 farver_2.1.1 -## [25] stringr_1.5.0 textshaping_0.3.6 munsell_0.5.0 htmltools_0.5.6 -## [29] sass_0.4.7 yaml_2.3.7 lazyeval_0.2.2 plotly_4.10.1 -## [33] pillar_1.9.0 pkgdown_2.0.7 jquerylib_0.1.4 tidyr_1.3.0 -## [37] MASS_7.3-60 cachem_1.0.8 nlme_3.1-163 tidyselect_1.2.0 -## [41] conflicted_1.2.0 digest_0.6.33 stringi_1.7.12 dplyr_1.1.3 -## [45] purrr_1.0.2 splines_4.3.2 labeling_0.4.3 forcats_1.0.0 -## [49] rprojroot_2.0.3 fastmap_1.1.1 grid_4.3.2 colorspace_2.1-0 -## [53] cli_3.6.1 magrittr_2.0.3 utf8_1.2.3 withr_2.5.1 -## [57] scales_1.2.1 rmarkdown_2.25 httr_1.4.7 gridExtra_2.3 -## [61] cellranger_1.1.0 ragg_1.2.5 memoise_2.0.1 evaluate_0.21 -## [65] knitr_1.44 viridisLite_0.4.2 mgcv_1.9-0 rlang_1.1.1 -## [69] Rcpp_1.0.11 glue_1.6.2 jsonlite_1.8.7 R6_2.5.1 -## [73] systemfonts_1.0.4 fs_1.6.3 +## [1] gtable_0.3.4 xfun_0.42 bslib_0.6.1 ggplot2_3.5.0 +## [5] htmlwidgets_1.6.4 ggrepel_0.9.5 lattice_0.22-5 vctrs_0.6.5 +## [9] tools_4.3.2 generics_0.1.3 tibble_3.2.1 fansi_1.0.6 +## [13] highr_0.10 pkgconfig_2.0.3 KernSmooth_2.23-22 Matrix_1.6-5 +## [17] pheatmap_1.0.12 data.table_1.15.2 RColorBrewer_1.1-3 desc_1.4.3 +## [21] readxl_1.4.3 lifecycle_1.0.4 prolfqua_1.1.5 compiler_4.3.2 +## [25] farver_2.1.1 stringr_1.5.1 textshaping_0.3.7 munsell_0.5.0 +## [29] htmltools_0.5.7 sass_0.4.8 yaml_2.3.8 lazyeval_0.2.2 +## [33] plotly_4.10.4 pillar_1.9.0 pkgdown_2.0.7 jquerylib_0.1.4 +## [37] tidyr_1.3.1 MASS_7.3-60.0.1 cachem_1.0.8 nlme_3.1-164 +## [41] tidyselect_1.2.0 conflicted_1.2.0 digest_0.6.34 stringi_1.8.3 +## [45] dplyr_1.1.4 purrr_1.0.2 labeling_0.4.3 forcats_1.0.0 +## [49] splines_4.3.2 fastmap_1.1.1 grid_4.3.2 colorspace_2.1-0 +## [53] cli_3.6.2 magrittr_2.0.3 utf8_1.2.4 withr_3.0.0 +## [57] scales_1.3.0 rmarkdown_2.26 httr_1.4.7 gridExtra_2.3 +## [61] cellranger_1.1.0 ragg_1.2.7 memoise_2.0.1 evaluate_0.23 +## [65] knitr_1.45 viridisLite_0.4.2 mgcv_1.9-1 rlang_1.1.3 +## [69] Rcpp_1.0.12 glue_1.7.0 jsonlite_1.8.8 R6_2.5.1 +## [73] systemfonts_1.0.6 fs_1.6.3

References diff --git a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/checkForHeteroskedasticity-1.png b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/checkForHeteroskedasticity-1.png index cb72c23b2..6c5d7a1d1 100644 Binary files a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/checkForHeteroskedasticity-1.png and b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/checkForHeteroskedasticity-1.png differ diff --git a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/cvDistr-1.png b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/cvDistr-1.png index a273876bb..deffb3198 100644 Binary files a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/cvDistr-1.png and b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/cvDistr-1.png differ diff --git a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/doPCA-1.png b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/doPCA-1.png index ba145ef94..962c26a08 100644 Binary files a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/doPCA-1.png and b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/doPCA-1.png differ diff --git a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/intensityDistribution-1.png b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/intensityDistribution-1.png index 713b022a7..f4884b597 100644 Binary files a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/intensityDistribution-1.png and b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/intensityDistribution-1.png differ diff --git a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/missingnessHist-1.png b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/missingnessHist-1.png index f60a1b977..86664c896 100644 Binary files a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/missingnessHist-1.png and b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/missingnessHist-1.png differ diff --git a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/plotDensities-1.png b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/plotDensities-1.png index ca3f0410a..f84c1bc25 100644 Binary files a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/plotDensities-1.png and b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/plotDensities-1.png differ diff --git a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/plotScatterMatrix-1.png b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/plotScatterMatrix-1.png index 204cd2390..30a23fc79 100644 Binary files a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/plotScatterMatrix-1.png and b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/plotScatterMatrix-1.png differ diff --git a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/sddensity-1.png b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/sddensity-1.png index 1be09b40b..020cdc456 100644 Binary files a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/sddensity-1.png and b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/sddensity-1.png differ diff --git a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/stdvVSmean-1.png b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/stdvVSmean-1.png index 2fa903f3c..88982781e 100644 Binary files a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/stdvVSmean-1.png and b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/stdvVSmean-1.png differ diff --git a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/unnamed-chunk-2-1.png b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/unnamed-chunk-2-1.png index ad717071b..901ea82f4 100644 Binary files a/articles/QualityControlAndSampleSizeEstimation_files/figure-html/unnamed-chunk-2-1.png and b/articles/QualityControlAndSampleSizeEstimation_files/figure-html/unnamed-chunk-2-1.png differ diff --git a/articles/SimulateData.html b/articles/SimulateData.html index d0c4c32e9..a98bfd676 100644 --- a/articles/SimulateData.html +++ b/articles/SimulateData.html @@ -109,7 +109,7 @@

Simulate Peptide level Data

Witold E. Wolski

-

2024-01-23

+

2024-03-20

Source: vignettes/SimulateData.Rmd @@ -190,7 +190,7 @@

Analyse simulated data with prolfq 
## # A tibble: 1 × 3
 ##   isotopeLabel protein_Id peptide_Id
 ##   <chr>             <int>      <int>
-## 1 light                16         73
+## 1 light 13 53 
 lfqdata$config$table$hierarchy_keys_depth()
## [1] "protein_Id"
diff --git a/articles/SimulateData_files/figure-html/unnamed-chunk-4-1.png b/articles/SimulateData_files/figure-html/unnamed-chunk-4-1.png index 1681ee5bd..46aeb8ec3 100644 Binary files a/articles/SimulateData_files/figure-html/unnamed-chunk-4-1.png and b/articles/SimulateData_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/articles/SimulateData_files/figure-html/unnamed-chunk-5-1.png b/articles/SimulateData_files/figure-html/unnamed-chunk-5-1.png index 5076d9660..6b803a886 100644 Binary files a/articles/SimulateData_files/figure-html/unnamed-chunk-5-1.png and b/articles/SimulateData_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/articles/SimulateData_files/figure-html/unnamed-chunk-6-1.png b/articles/SimulateData_files/figure-html/unnamed-chunk-6-1.png index 415fbab12..181d22ed4 100644 Binary files a/articles/SimulateData_files/figure-html/unnamed-chunk-6-1.png and b/articles/SimulateData_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/articles/SimulateData_files/figure-html/unnamed-chunk-8-1.png b/articles/SimulateData_files/figure-html/unnamed-chunk-8-1.png index e9db2e573..0e1acdc13 100644 Binary files a/articles/SimulateData_files/figure-html/unnamed-chunk-8-1.png and b/articles/SimulateData_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/articles/Supplement_TidyAnalysis_HL_Skyline.html b/articles/Supplement_TidyAnalysis_HL_Skyline.html index f743db781..8da8a091d 100644 --- a/articles/Supplement_TidyAnalysis_HL_Skyline.html +++ b/articles/Supplement_TidyAnalysis_HL_Skyline.html @@ -110,7 +110,7 @@

Supplement - Data preprocessing of SRM Heavy

Functional Genomics Center Zurich

-

23 January, 2024

+

20 March, 2024

Source: vignettes/Supplement_TidyAnalysis_HL_Skyline.Rmd @@ -120,7 +120,7 @@

23 January, 2024

-rm(list = ls())
+rm(list = ls())
 library(conflicted)
 library(prolfqua)
diff --git a/articles/Supplement_TidyAnalysis_HL_Skyline_files/figure-html/plotHierarchies-1.png b/articles/Supplement_TidyAnalysis_HL_Skyline_files/figure-html/plotHierarchies-1.png
index 85b603d5e..92a94b8f8 100644
Binary files a/articles/Supplement_TidyAnalysis_HL_Skyline_files/figure-html/plotHierarchies-1.png and b/articles/Supplement_TidyAnalysis_HL_Skyline_files/figure-html/plotHierarchies-1.png differ
diff --git a/articles/Supplement_TidyAnalysis_HL_Skyline_files/figure-html/plotProteinIntensitiesFreeY-1.png b/articles/Supplement_TidyAnalysis_HL_Skyline_files/figure-html/plotProteinIntensitiesFreeY-1.png
index 4c53ca68b..a98b1a332 100644
Binary files a/articles/Supplement_TidyAnalysis_HL_Skyline_files/figure-html/plotProteinIntensitiesFreeY-1.png and b/articles/Supplement_TidyAnalysis_HL_Skyline_files/figure-html/plotProteinIntensitiesFreeY-1.png differ
diff --git a/articles/Supplement_TidyAnalysis_Skyline_PRM.html b/articles/Supplement_TidyAnalysis_Skyline_PRM.html
index f12ef592d..92a6f895f 100644
--- a/articles/Supplement_TidyAnalysis_Skyline_PRM.html
+++ b/articles/Supplement_TidyAnalysis_Skyline_PRM.html
@@ -109,7 +109,7 @@ 
Supplement - Data preprocessing for PRM

                         
Functional
 Genomics Center Zurich

             
-            
23 January, 2024

+            
20 March, 2024

       
       Source: vignettes/Supplement_TidyAnalysis_Skyline_PRM.Rmd
       
@@ -121,7 +121,7 @@ 
23 January, 2024

 
Example of visualizing and normalizing PRM data using an internal
 CiRT peptides (S. Parker 2015 MCP).

 
-rm(list = ls())
+rm(list = ls())
 library(conflicted)
 library(readxl)
 library(yaml)
diff --git a/articles/Supplement_TidyAnalysis_Skyline_PRM_files/figure-html/plotProtQuants-1.png b/articles/Supplement_TidyAnalysis_Skyline_PRM_files/figure-html/plotProtQuants-1.png
index 63a8acebd..87a95537b 100644
Binary files a/articles/Supplement_TidyAnalysis_Skyline_PRM_files/figure-html/plotProtQuants-1.png and b/articles/Supplement_TidyAnalysis_Skyline_PRM_files/figure-html/plotProtQuants-1.png differ
diff --git a/articles/Supplement_TidyCorrelationAnalysis.html b/articles/Supplement_TidyCorrelationAnalysis.html
index 6da6a799b..a34a644bc 100644
--- a/articles/Supplement_TidyCorrelationAnalysis.html
+++ b/articles/Supplement_TidyCorrelationAnalysis.html
@@ -110,7 +110,7 @@ 
Supplement - Filter precursors or fragments
                         
Functional
 Genomics Center Zurich

             
-            
23 January, 2024

+            
20 March, 2024

       
       Source: vignettes/Supplement_TidyCorrelationAnalysis.Rmd
       
@@ -124,7 +124,7 @@ 
23 January, 2024

 prolfqua.

 
First we load the required packages.

 
-rm(list = ls())
+rm(list = ls())
 
 library(conflicted)
 library(dplyr)
@@ -147,7 +147,7 @@ 
23 January, 2024

 
 data("data_spectronautDIA250_A")
 longFormat <- data_spectronautDIA250_A$data
-"PEP.StrippedSequence" %in% colnames(longFormat)

+"PEP.StrippedSequence" %in% colnames(longFormat)

 
## [1] TRUE

 
 longFormat$Isotope.Label <- "Light"
@@ -533,27 +533,27 @@ 
Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] prolfqua_1.1.5   ggplot2_3.4.4    dplyr_1.1.3      conflicted_1.2.0
+## [1] prolfqua_1.1.5   ggplot2_3.5.0    dplyr_1.1.4      conflicted_1.2.0
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] gtable_0.3.4       xfun_0.40          bslib_0.5.1        htmlwidgets_1.6.2 
-##  [5] ggrepel_0.9.3      lattice_0.21-9     vctrs_0.6.4        tools_4.3.2       
-##  [9] generics_0.1.3     tibble_3.2.1       fansi_1.0.5        pkgconfig_2.0.3   
-## [13] Matrix_1.6-1.1     pheatmap_1.0.12    data.table_1.14.8  RColorBrewer_1.1-3
-## [17] desc_1.4.2         lifecycle_1.0.3    farver_2.1.1       compiler_4.3.2    
-## [21] stringr_1.5.0      textshaping_0.3.6  munsell_0.5.0      htmltools_0.5.6   
-## [25] sass_0.4.7         yaml_2.3.7         lazyeval_0.2.2     plotly_4.10.1     
-## [29] nloptr_2.0.3       pillar_1.9.0       pkgdown_2.0.7      jquerylib_0.1.4   
-## [33] tidyr_1.3.0        MASS_7.3-60        cachem_1.0.8       boot_1.3-28.1     
-## [37] nlme_3.1-163       tidyselect_1.2.0   digest_0.6.33      stringi_1.7.12    
-## [41] purrr_1.0.2        labeling_0.4.3     forcats_1.0.0      splines_4.3.2     
-## [45] rprojroot_2.0.3    fastmap_1.1.1      grid_4.3.2         colorspace_2.1-0  
-## [49] cli_3.6.1          magrittr_2.0.3     utf8_1.2.3         withr_2.5.1       
-## [53] scales_1.2.1       rmarkdown_2.25     httr_1.4.7         lme4_1.1-33       
-## [57] gridExtra_2.3      ragg_1.2.5         memoise_2.0.1      evaluate_0.21     
-## [61] knitr_1.44         viridisLite_0.4.2  rlang_1.1.1        Rcpp_1.0.11       
-## [65] glue_1.6.2         minqa_1.2.5        jsonlite_1.8.7     R6_2.5.1          
-## [69] systemfonts_1.0.4  fs_1.6.3

+##  [1] gtable_0.3.4       xfun_0.42          bslib_0.6.1        htmlwidgets_1.6.4 
+##  [5] ggrepel_0.9.5      lattice_0.22-5     vctrs_0.6.5        tools_4.3.2       
+##  [9] generics_0.1.3     tibble_3.2.1       fansi_1.0.6        highr_0.10        
+## [13] pkgconfig_2.0.3    pheatmap_1.0.12    Matrix_1.6-5       data.table_1.15.2 
+## [17] RColorBrewer_1.1-3 desc_1.4.3         lifecycle_1.0.4    compiler_4.3.2    
+## [21] farver_2.1.1       stringr_1.5.1      textshaping_0.3.7  munsell_0.5.0     
+## [25] htmltools_0.5.7    sass_0.4.8         yaml_2.3.8         lazyeval_0.2.2    
+## [29] plotly_4.10.4      pillar_1.9.0       pkgdown_2.0.7      nloptr_2.0.3      
+## [33] jquerylib_0.1.4    tidyr_1.3.1        MASS_7.3-60.0.1    cachem_1.0.8      
+## [37] boot_1.3-30        nlme_3.1-164       tidyselect_1.2.0   digest_0.6.34     
+## [41] stringi_1.8.3      purrr_1.0.2        labeling_0.4.3     forcats_1.0.0     
+## [45] splines_4.3.2      fastmap_1.1.1      grid_4.3.2         colorspace_2.1-0  
+## [49] cli_3.6.2          magrittr_2.0.3     utf8_1.2.4         withr_3.0.0       
+## [53] scales_1.3.0       rmarkdown_2.26     httr_1.4.7         lme4_1.1-35.1     
+## [57] gridExtra_2.3      ragg_1.2.7         memoise_2.0.1      evaluate_0.23     
+## [61] knitr_1.45         viridisLite_0.4.2  rlang_1.1.3        Rcpp_1.0.12       
+## [65] glue_1.7.0         minqa_1.2.6        jsonlite_1.8.8     R6_2.5.1          
+## [69] systemfonts_1.0.6  fs_1.6.3

 

 

 
References
diff --git a/articles/Supplement_TidyCorrelationAnalysis_files/figure-html/shownotcorrelated-1.png b/articles/Supplement_TidyCorrelationAnalysis_files/figure-html/shownotcorrelated-1.png
index 18a9c606c..4bace515e 100644
Binary files a/articles/Supplement_TidyCorrelationAnalysis_files/figure-html/shownotcorrelated-1.png and b/articles/Supplement_TidyCorrelationAnalysis_files/figure-html/shownotcorrelated-1.png differ
diff --git a/articles/Supplement_TidyCorrelationAnalysis_files/figure-html/shownotcorrelated-2.png b/articles/Supplement_TidyCorrelationAnalysis_files/figure-html/shownotcorrelated-2.png
index abcf0b31f..cd870d22d 100644
Binary files a/articles/Supplement_TidyCorrelationAnalysis_files/figure-html/shownotcorrelated-2.png and b/articles/Supplement_TidyCorrelationAnalysis_files/figure-html/shownotcorrelated-2.png differ
diff --git a/articles/Supplement_TidyCorrelationAnalysis_files/figure-html/shownotcorrelated-3.png b/articles/Supplement_TidyCorrelationAnalysis_files/figure-html/shownotcorrelated-3.png
index 26da893ea..02652e8a6 100644
Binary files a/articles/Supplement_TidyCorrelationAnalysis_files/figure-html/shownotcorrelated-3.png and b/articles/Supplement_TidyCorrelationAnalysis_files/figure-html/shownotcorrelated-3.png differ
diff --git a/articles/Supplement_srm_summary.html b/articles/Supplement_srm_summary.html
index 1d3b026de..e8f50e878 100644
--- a/articles/Supplement_srm_summary.html
+++ b/articles/Supplement_srm_summary.html
@@ -109,7 +109,7 @@ 
Supplement - Summarize SRM Peptide Level
 Measurements

                         

             
-            
2024-01-23

+            
2024-03-20

       
       Source: vignettes/Supplement_srm_summary.Rmd
       
diff --git a/articles/Supplement_srm_summary_HL.html b/articles/Supplement_srm_summary_HL.html
index a940a08df..dba9e1c0d 100644
--- a/articles/Supplement_srm_summary_HL.html
+++ b/articles/Supplement_srm_summary_HL.html
@@ -109,7 +109,7 @@ 
Supplement - Summarize heavy light Peptide Level
 Measurements

                         

             
-            
2024-01-23

+            
2024-03-20

       
       Source: vignettes/Supplement_srm_summary_HL.Rmd
       
diff --git a/articles/Supplement_srm_summary_HL_files/figure-html/missingFigIntensityHistorgram-1.png b/articles/Supplement_srm_summary_HL_files/figure-html/missingFigIntensityHistorgram-1.png
index 392149a1c..85adaa93a 100644
Binary files a/articles/Supplement_srm_summary_HL_files/figure-html/missingFigIntensityHistorgram-1.png and b/articles/Supplement_srm_summary_HL_files/figure-html/missingFigIntensityHistorgram-1.png differ
diff --git a/articles/Supplement_srm_summary_files/figure-html/missingFigIntensityHistorgram-1.png b/articles/Supplement_srm_summary_files/figure-html/missingFigIntensityHistorgram-1.png
index 784582ed3..4c291b901 100644
Binary files a/articles/Supplement_srm_summary_files/figure-html/missingFigIntensityHistorgram-1.png and b/articles/Supplement_srm_summary_files/figure-html/missingFigIntensityHistorgram-1.png differ
diff --git a/pkgdown.yml b/pkgdown.yml
index 8787b4d03..8575a506c 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -13,5 +13,5 @@ articles:
   Supplement_TidyCorrelationAnalysis: Supplement_TidyCorrelationAnalysis.html
   Supplement_srm_summary: Supplement_srm_summary.html
   Supplement_srm_summary_HL: Supplement_srm_summary_HL.html
-last_built: 2024-01-23T12:51Z
+last_built: 2024-03-20T13:33Z
 
diff --git a/reference/Benchmark-1.png b/reference/Benchmark-1.png
index 5e4518e2a..b1cac91dc 100644
Binary files a/reference/Benchmark-1.png and b/reference/Benchmark-1.png differ
diff --git a/reference/Benchmark-2.png b/reference/Benchmark-2.png
index d50d4bb22..947cebb3c 100644
Binary files a/reference/Benchmark-2.png and b/reference/Benchmark-2.png differ
diff --git a/reference/Benchmark-3.png b/reference/Benchmark-3.png
index d82d0aade..a80ebbff8 100644
Binary files a/reference/Benchmark-3.png and b/reference/Benchmark-3.png differ
diff --git a/reference/Benchmark-4.png b/reference/Benchmark-4.png
index 4a1f3b9f6..643da63c3 100644
Binary files a/reference/Benchmark-4.png and b/reference/Benchmark-4.png differ
diff --git a/reference/Benchmark-5.png b/reference/Benchmark-5.png
index 6fea57452..2b611ab11 100644
Binary files a/reference/Benchmark-5.png and b/reference/Benchmark-5.png differ
diff --git a/reference/Benchmark-6.png b/reference/Benchmark-6.png
index b1311de73..d20b143c3 100644
Binary files a/reference/Benchmark-6.png and b/reference/Benchmark-6.png differ
diff --git a/reference/Benchmark-7.png b/reference/Benchmark-7.png
index ed6f0824f..e39fba198 100644
Binary files a/reference/Benchmark-7.png and b/reference/Benchmark-7.png differ
diff --git a/reference/Benchmark.html b/reference/Benchmark.html
index dce86f2fe..b6cb9e759 100644
--- a/reference/Benchmark.html
+++ b/reference/Benchmark.html
@@ -507,11 +507,14 @@ 
Examples

 medpol_benchmark$plot_score_distribution(list(list(score = "estimate", xlim = c(-1,2) ),
  list(score = "statistic", xlim = c(-3,10) )))
 #> Picking joint bandwidth of 0.023
-#> Warning: Removed 20 rows containing non-finite values (`stat_density_ridges()`).
+#> Warning: Removed 20 rows containing non-finite outside the scale range
+#> (`stat_density_ridges()`).
 #> Picking joint bandwidth of 0.023
-#> Warning: Removed 20 rows containing non-finite values (`stat_density_ridges()`).
+#> Warning: Removed 20 rows containing non-finite outside the scale range
+#> (`stat_density_ridges()`).
 #> Picking joint bandwidth of 0.37
-#> Warning: Removed 172 rows containing non-finite values (`stat_density_ridges()`).
+#> Warning: Removed 172 rows containing non-finite outside the scale range
+#> (`stat_density_ridges()`).
 
 medpol_benchmark$get_confusion_benchmark()
 #> # A tibble: 97,398 × 19
@@ -562,11 +565,14 @@ 
Examples

 #> 4          3         11
 benchmark$plot_score_distribution(list(list(score = "estimate", xlim = c(-1,2) ),list(score = "statistic", xlim = c(-3,10) )))
 #> Picking joint bandwidth of 0.023
-#> Warning: Removed 20 rows containing non-finite values (`stat_density_ridges()`).
+#> Warning: Removed 20 rows containing non-finite outside the scale range
+#> (`stat_density_ridges()`).
 #> Picking joint bandwidth of 0.023
-#> Warning: Removed 20 rows containing non-finite values (`stat_density_ridges()`).
+#> Warning: Removed 20 rows containing non-finite outside the scale range
+#> (`stat_density_ridges()`).
 #> Picking joint bandwidth of 0.37
-#> Warning: Removed 172 rows containing non-finite values (`stat_density_ridges()`).
+#> Warning: Removed 172 rows containing non-finite outside the scale range
+#> (`stat_density_ridges()`).
 
 benchmark$plot_score_distribution()
 #> Picking joint bandwidth of 0.0231
@@ -583,18 +589,23 @@ 
Examples

 
 
 benchmark$plot_ROC(xlim = 0.1)
-#> Warning: Removed 12784 rows containing missing values (`geom_path()`).
+#> Warning: Removed 12784 rows containing missing values or values outside the scale range
+#> (`geom_path()`).
 
 benchmark$plot_precision_recall()
-#> Warning: Removed 13479 rows containing missing values (`geom_path()`).
+#> Warning: Removed 13479 rows containing missing values or values outside the scale range
+#> (`geom_path()`).
 
 
 benchmark$plot_FDRvsFDP()
 
 benchmark$plot_scatter(list(list(score = "estimate", ylim = c(-1,2) ),list(score = "statistic", ylim = c(-3,10) )))
-#> Warning: Removed 20 rows containing missing values (`geom_point()`).
-#> Warning: Removed 20 rows containing missing values (`geom_point()`).
-#> Warning: Removed 172 rows containing missing values (`geom_point()`).
+#> Warning: Removed 20 rows containing missing values or values outside the scale range
+#> (`geom_point()`).
+#> Warning: Removed 20 rows containing missing values or values outside the scale range
+#> (`geom_point()`).
+#> Warning: Removed 172 rows containing missing values or values outside the scale range
+#> (`geom_point()`).
 
 benchmark$complete(FALSE)
 benchmark$missing_contrasts()
diff --git a/reference/Contrasts.html b/reference/Contrasts.html
index 034d48aa9..319ac7b9c 100644
--- a/reference/Contrasts.html
+++ b/reference/Contrasts.html
@@ -100,7 +100,6 @@ 
See also

 ContrastsPlotter,
 ContrastsProDA,
 ContrastsROPECA,
-ContrastsSAINTexpress,
 ContrastsTable,
 INTERNAL_FUNCTIONS_BY_FAMILY,
 LR_test(),
@@ -119,12 +118,12 @@ 
See also

 merge_contrasts_results(),
 model_analyse(),
 model_summary(),
-moderated_p_limma_long(),
 moderated_p_limma(),
+moderated_p_limma_long(),
 my_contest(),
+my_contrast(),
 my_contrast_V1(),
 my_contrast_V2(),
-my_contrast(),
 my_glht(),
 pivot_model_contrasts_2_Wide(),
 plot_lmer_model_and_data(),
@@ -437,7 +436,6 @@ 
Examples

 #> boundary (singular) fit: see help('isSingular')
 #> boundary (singular) fit: see help('isSingular')
 #> boundary (singular) fit: see help('isSingular')
-#> boundary (singular) fit: see help('isSingular')
 #> Warning: There was 1 warning in `dplyr::mutate()`.
 #> ℹ In argument: `linear_model = purrr::map(data, model_strategy$model_fun, pb =
 #>   pb)`.
@@ -455,7 +453,7 @@ 
Examples

 #> $isSingular
 #> 
 #> FALSE  TRUE 
-#>    79    83 
+#>    80    82 
 #> 
  Contr <- c("dil.a_vs_b" = "dilution.a - dilution.b",
     "dil.e_vs_b" = "dilution.e - dilution.b" )
diff --git a/reference/ContrastsMissing.html b/reference/ContrastsMissing.html
index 11a69d796..36053d424 100644
--- a/reference/ContrastsMissing.html
+++ b/reference/ContrastsMissing.html
@@ -105,13 +105,12 @@ 
Details

     

     
See also

     
Other modelling: 
+Contrasts,
 ContrastsModerated,
 ContrastsPlotter,
 ContrastsProDA,
 ContrastsROPECA,
-ContrastsSAINTexpress,
 ContrastsTable,
-Contrasts,
 INTERNAL_FUNCTIONS_BY_FAMILY,
 LR_test(),
 Model,
@@ -129,12 +128,12 @@ 
See also

 merge_contrasts_results(),
 model_analyse(),
 model_summary(),
-moderated_p_limma_long(),
 moderated_p_limma(),
+moderated_p_limma_long(),
 my_contest(),
+my_contrast(),
 my_contrast_V1(),
 my_contrast_V2(),
-my_contrast(),
 my_glht(),
 pivot_model_contrasts_2_Wide(),
 plot_lmer_model_and_data(),
diff --git a/reference/ContrastsModerated-1.png b/reference/ContrastsModerated-1.png
index 0d5c904f2..d7389edaa 100644
Binary files a/reference/ContrastsModerated-1.png and b/reference/ContrastsModerated-1.png differ
diff --git a/reference/ContrastsModerated-2.png b/reference/ContrastsModerated-2.png
index fa4a2b050..c7a8190ad 100644
Binary files a/reference/ContrastsModerated-2.png and b/reference/ContrastsModerated-2.png differ
diff --git a/reference/ContrastsModerated-3.png b/reference/ContrastsModerated-3.png
index c42dae40e..84238c364 100644
Binary files a/reference/ContrastsModerated-3.png and b/reference/ContrastsModerated-3.png differ
diff --git a/reference/ContrastsModerated-4.png b/reference/ContrastsModerated-4.png
index 85e688650..55c80066f 100644
Binary files a/reference/ContrastsModerated-4.png and b/reference/ContrastsModerated-4.png differ
diff --git a/reference/ContrastsModerated.html b/reference/ContrastsModerated.html
index fbfef1772..21d0261eb 100644
--- a/reference/ContrastsModerated.html
+++ b/reference/ContrastsModerated.html
@@ -96,13 +96,12 @@ 
Limma moderated contrasts

     
See also

     
moderated_p_limma_long

 
Other modelling: 
+Contrasts,
 ContrastsMissing,
 ContrastsPlotter,
 ContrastsProDA,
 ContrastsROPECA,
-ContrastsSAINTexpress,
 ContrastsTable,
-Contrasts,
 INTERNAL_FUNCTIONS_BY_FAMILY,
 LR_test(),
 Model,
@@ -120,12 +119,12 @@ 
See also

 merge_contrasts_results(),
 model_analyse(),
 model_summary(),
-moderated_p_limma_long(),
 moderated_p_limma(),
+moderated_p_limma_long(),
 my_contest(),
+my_contrast(),
 my_contrast_V1(),
 my_contrast_V2(),
-my_contrast(),
 my_glht(),
 pivot_model_contrasts_2_Wide(),
 plot_lmer_model_and_data(),
@@ -308,25 +307,23 @@ 
Arguments
     
Examples

     

-istar <- prolfqua_data('data_ionstar')$normalized()
-istar$config <- old2new(istar$config)
-istar_data <- dplyr::filter(istar$data ,protein_Id %in% sample(protein_Id, 100))
-pepIntensity <- istar_data
-config <- istar$config$clone(deep = TRUE)
+istar <- sim_lfq_data_protein_config(Nprot = 50)
+#> sample already exists
+#> completing cases
+protIntensity <- istar$data
+config <- istar$config
 
 
-ld <- LFQData$new(pepIntensity, config)
-lProt <- ld$get_Aggregator()$medpolish()
-#> starting aggregation
+lProt <- LFQData$new(protIntensity, config)
 lProt$rename_response("transformedIntensity")
 modelFunction <-
-  strategy_lm("transformedIntensity  ~ dilution.")
+  strategy_lm("transformedIntensity  ~ group_")
 mod <- build_model(
  lProt,
  modelFunction)
 #> Joining with `by = join_by(protein_Id)`
 
-Contr <- c("dil.b_vs_a" = "dilution.a - dilution.b")
+Contr <- c("dil.b_vs_a" = "group_A - group_Ctrl")
 contrast <- prolfqua::Contrasts$new(mod,
  Contr)
 contrast <- ContrastsModerated$new(contrast)
@@ -340,8 +337,8 @@ 
Examples

 
 merged <- merge_contrasts_results(contrast, csi)
 #> completing cases
-#> dil.b_vs_a=dilution.a - dilution.b
-#> dil.b_vs_a=dilution.a - dilution.b
+#> dil.b_vs_a=group_A - group_Ctrl
+#> dil.b_vs_a=group_A - group_Ctrl
 #> Joining with `by = join_by(protein_Id, contrast)`
 #> completing cases
 #> Joining with `by = join_by(protein_Id, contrast)`
@@ -349,23 +346,20 @@ 
Examples

 
 merged$more$get_contrasts() |> dim()
 #> [1]  0 13
-merged$merged$get_contrasts() |> dim()
-#> [1] 60 13
-merged$same$get_contrasts() |> dim()
-#> [1] 60 13
+stopifnot(all(dim(merged$merged$get_contrasts() == c(50,13))))
+stopifnot(all(dim(merged$same$get_contrasts()) == c(50,13)))
 
 cs <- contrast$get_contrast_sides()
 cslf <- contrast$get_linfct()
 ctr <- contrast$get_contrasts()
 ctrwide <- contrast$to_wide()
 cp <- contrast$get_Plotter()
-cp$histogram()
-#> $p.value
+
+print(cp$histogram()$p.value, vp=NULL)
 
-#> 
-#> $FDR
+print(cp$histogram()$FDR, vp = NULL)
 
-#> 
+
 cp$volcano()
 #> $FDR
 
diff --git a/reference/ContrastsPlotter.html b/reference/ContrastsPlotter.html
index dc7178cb6..11ee78af2 100644
--- a/reference/ContrastsPlotter.html
+++ b/reference/ContrastsPlotter.html
@@ -95,13 +95,12 @@ 
plot contrasts

     

     
See also

     
Other modelling: 
+Contrasts,
 ContrastsMissing,
 ContrastsModerated,
 ContrastsProDA,
 ContrastsROPECA,
-ContrastsSAINTexpress,
 ContrastsTable,
-Contrasts,
 INTERNAL_FUNCTIONS_BY_FAMILY,
 LR_test(),
 Model,
@@ -119,12 +118,12 @@ 
See also

 merge_contrasts_results(),
 model_analyse(),
 model_summary(),
-moderated_p_limma_long(),
 moderated_p_limma(),
+moderated_p_limma_long(),
 my_contest(),
+my_contrast(),
 my_contrast_V1(),
 my_contrast_V2(),
-my_contrast(),
 my_glht(),
 pivot_model_contrasts_2_Wide(),
 plot_lmer_model_and_data(),
@@ -139,16 +138,16 @@ 
See also

 UpSet_missing_stats(),
 medpolish_estimate_df(),
 missigness_histogram(),
-missingness_per_condition_cumsum(),
 missingness_per_condition(),
+missingness_per_condition_cumsum(),
 plot_NA_heatmap(),
 plot_estimate(),
-plot_heatmap_cor(),
 plot_heatmap(),
+plot_heatmap_cor(),
 plot_hierarchies_add_quantline(),
 plot_hierarchies_boxplot_df(),
-plot_hierarchies_line_df(),
 plot_hierarchies_line(),
+plot_hierarchies_line_df(),
 plot_intensity_distribution_violin(),
 plot_pca(),
 plot_raster(),
@@ -351,6 +350,10 @@ 
ArgumentsArguments
diff --git a/reference/ContrastsProDA-1.png b/reference/ContrastsProDA-1.png
index 9053cb207..08436a8d4 100644
Binary files a/reference/ContrastsProDA-1.png and b/reference/ContrastsProDA-1.png differ
diff --git a/reference/ContrastsProDA-2.png b/reference/ContrastsProDA-2.png
index 6bd630507..3ee0e22ee 100644
Binary files a/reference/ContrastsProDA-2.png and b/reference/ContrastsProDA-2.png differ
diff --git a/reference/ContrastsProDA.html b/reference/ContrastsProDA.html
index 7549ed44c..2a3e04284 100644
--- a/reference/ContrastsProDA.html
+++ b/reference/ContrastsProDA.html
@@ -95,13 +95,12 @@ 
ContrastsProDA Wrapper to results produced by proDA

     

     
See also

     
Other modelling: 
+Contrasts,
 ContrastsMissing,
 ContrastsModerated,
 ContrastsPlotter,
 ContrastsROPECA,
-ContrastsSAINTexpress,
 ContrastsTable,
-Contrasts,
 INTERNAL_FUNCTIONS_BY_FAMILY,
 LR_test(),
 Model,
@@ -119,12 +118,12 @@ 
See also

 merge_contrasts_results(),
 model_analyse(),
 model_summary(),
-moderated_p_limma_long(),
 moderated_p_limma(),
+moderated_p_limma_long(),
 my_contest(),
+my_contrast(),
 my_contrast_V1(),
 my_contrast_V2(),
-my_contrast(),
 my_glht(),
 pivot_model_contrasts_2_Wide(),
 plot_lmer_model_and_data(),
diff --git a/reference/ContrastsROPECA-3.png b/reference/ContrastsROPECA-3.png
index 0c16fdc48..492a4f697 100644
Binary files a/reference/ContrastsROPECA-3.png and b/reference/ContrastsROPECA-3.png differ
diff --git a/reference/ContrastsROPECA.html b/reference/ContrastsROPECA.html
index 312deb84d..2f2127276 100644
--- a/reference/ContrastsROPECA.html
+++ b/reference/ContrastsROPECA.html
@@ -102,13 +102,12 @@ 
Details

     
See also

     
summary_ROPECA_median_p.scaled

 
Other modelling: 
+Contrasts,
 ContrastsMissing,
 ContrastsModerated,
 ContrastsPlotter,
 ContrastsProDA,
-ContrastsSAINTexpress,
 ContrastsTable,
-Contrasts,
 INTERNAL_FUNCTIONS_BY_FAMILY,
 LR_test(),
 Model,
@@ -126,12 +125,12 @@ 
See also

 merge_contrasts_results(),
 model_analyse(),
 model_summary(),
-moderated_p_limma_long(),
 moderated_p_limma(),
+moderated_p_limma_long(),
 my_contest(),
+my_contrast(),
 my_contrast_V1(),
 my_contrast_V2(),
-my_contrast(),
 my_glht(),
 pivot_model_contrasts_2_Wide(),
 plot_lmer_model_and_data(),
@@ -347,7 +346,7 @@ 
Examples

 #> The first warning was:
 #> ℹ In argument: `linear_model = purrr::map(data, model_strategy$model_fun, pb =
 #>   pb)`.
-#> ℹ In group 29: `protein_Id = "CON__P02769~18~NA"`, `peptide_Id =
+#> ℹ In group 29: `protein_Id = "CON__P02769~18~NA"` and `peptide_Id =
 #>   "VHKECCHGDLLECADDR"`.
 #> Caused by warning in `value[[3L]]()`:
 #> ! WARN :Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]): contrasts can be applied only to factors with 2 or more levels
@@ -420,15 +419,16 @@ 
Examples

 #> 1 dil.b_vs_a dilution.b dilution.a
  pl$histogram()
 #> $beta.based.significance
-#> Warning: Removed 1 rows containing non-finite values (`stat_bin()`).
+#> Warning: Removed 1 row containing non-finite outside the scale range (`stat_bin()`).
 
 #> 
 #> $FDR.beta.based.significance
-#> Warning: Removed 1 rows containing non-finite values (`stat_bin()`).
+#> Warning: Removed 1 row containing non-finite outside the scale range (`stat_bin()`).
 
 #> 
  pl$ma_plot()
-#> Warning: Removed 1 rows containing missing values (`geom_point()`).
+#> Warning: Removed 1 row containing missing values or values outside the scale range
+#> (`geom_point()`).
 
 
 

diff --git a/reference/ContrastsTable-1.png b/reference/ContrastsTable-1.png
index 692302663..4410ee4e9 100644
Binary files a/reference/ContrastsTable-1.png and b/reference/ContrastsTable-1.png differ
diff --git a/reference/ContrastsTable-2.png b/reference/ContrastsTable-2.png
index ef07683ca..d4b86fccf 100644
Binary files a/reference/ContrastsTable-2.png and b/reference/ContrastsTable-2.png differ
diff --git a/reference/ContrastsTable.html b/reference/ContrastsTable.html
index b822caf5a..e9a77dd01 100644
--- a/reference/ContrastsTable.html
+++ b/reference/ContrastsTable.html
@@ -96,13 +96,12 @@ 
holds results when contrasts are added.

     
See also

     
summary_ROPECA_median_p.scaled

 
Other modelling: 
+Contrasts,
 ContrastsMissing,
 ContrastsModerated,
 ContrastsPlotter,
 ContrastsProDA,
 ContrastsROPECA,
-ContrastsSAINTexpress,
-Contrasts,
 INTERNAL_FUNCTIONS_BY_FAMILY,
 LR_test(),
 Model,
@@ -120,12 +119,12 @@ 
See also

 merge_contrasts_results(),
 model_analyse(),
 model_summary(),
-moderated_p_limma_long(),
 moderated_p_limma(),
+moderated_p_limma_long(),
 my_contest(),
+my_contrast(),
 my_contrast_V1(),
 my_contrast_V2(),
-my_contrast(),
 my_glht(),
 pivot_model_contrasts_2_Wide(),
 plot_lmer_model_and_data(),
diff --git a/reference/FragPipe.html b/reference/FragPipe.html
index bc1d8943a..f794a752d 100644
--- a/reference/FragPipe.html
+++ b/reference/FragPipe.html
@@ -95,8 +95,8 @@ 
See also

     
Other FragPipe: 
 INTERNAL_FUNCTIONS_BY_FAMILY,
 tidy_FragPipe_MSstats_csv(),
-tidy_FragPipe_combined_protein_deprec(),
-tidy_FragPipe_combined_protein()

+tidy_FragPipe_combined_protein(),
+tidy_FragPipe_combined_protein_deprec()

     

 
   

diff --git a/reference/INTERNAL_FUNCTIONS_BY_FAMILY.html b/reference/INTERNAL_FUNCTIONS_BY_FAMILY.html
index 277d6d792..127c6c13c 100644
--- a/reference/INTERNAL_FUNCTIONS_BY_FAMILY.html
+++ b/reference/INTERNAL_FUNCTIONS_BY_FAMILY.html
@@ -96,16 +96,16 @@ 
See also

 aggregate_intensity_topN(),
 estimate_intensity(),
 intensity_summary_by_hkeys(),
-medpolish_estimate_dfconfig(),
-medpolish_estimate_df(),
 medpolish_estimate(),
+medpolish_estimate_df(),
+medpolish_estimate_dfconfig(),
 medpolish_protein_estimates(),
 plot_estimate(),
 plot_hierarchies_add_quantline(),
-plot_hierarchies_line_df(),
 plot_hierarchies_line(),
-rlm_estimate_dfconfig(),
-rlm_estimate()

+plot_hierarchies_line_df(),
+rlm_estimate(),
+rlm_estimate_dfconfig()

 
Other benchmarking: 
 Benchmark,
 ionstar_bench_preprocess(),
@@ -138,14 +138,13 @@ 
See also

 tidyMQ_Peptides(),
 tidyMQ_ProteinGroups()

 
Other modelling: 
+Contrasts,
 ContrastsMissing,
 ContrastsModerated,
 ContrastsPlotter,
 ContrastsProDA,
 ContrastsROPECA,
-ContrastsSAINTexpress,
 ContrastsTable,
-Contrasts,
 LR_test(),
 Model,
 build_model(),
@@ -162,12 +161,12 @@ 
See also

 merge_contrasts_results(),
 model_analyse(),
 model_summary(),
-moderated_p_limma_long(),
 moderated_p_limma(),
+moderated_p_limma_long(),
 my_contest(),
+my_contrast(),
 my_contrast_V1(),
 my_contrast_V2(),
-my_contrast(),
 my_glht(),
 pivot_model_contrasts_2_Wide(),
 plot_lmer_model_and_data(),
@@ -179,24 +178,24 @@ 
See also

 
Other FragPipe: 
 FragPipe,
 tidy_FragPipe_MSstats_csv(),
-tidy_FragPipe_combined_protein_deprec(),
-tidy_FragPipe_combined_protein()

+tidy_FragPipe_combined_protein(),
+tidy_FragPipe_combined_protein_deprec()

 
Other plotting: 
 ContrastsPlotter,
 UpSet_interaction_missing_stats(),
 UpSet_missing_stats(),
 medpolish_estimate_df(),
 missigness_histogram(),
-missingness_per_condition_cumsum(),
 missingness_per_condition(),
+missingness_per_condition_cumsum(),
 plot_NA_heatmap(),
 plot_estimate(),
-plot_heatmap_cor(),
 plot_heatmap(),
+plot_heatmap_cor(),
 plot_hierarchies_add_quantline(),
 plot_hierarchies_boxplot_df(),
-plot_hierarchies_line_df(),
 plot_hierarchies_line(),
+plot_hierarchies_line_df(),
 plot_intensity_distribution_violin(),
 plot_pca(),
 plot_raster(),
@@ -208,22 +207,22 @@ 
See also

 get_robscales(),
 normalize_log2_robscale(),
 robust_scale(),
-scale_with_subset_by_factors(),
-scale_with_subset()

+scale_with_subset(),
+scale_with_subset_by_factors()

 
Other stats: 
 lfq_power_t_test_proteins(),
-lfq_power_t_test_quantiles_V2(),
 lfq_power_t_test_quantiles(),
-plot_stat_density_median(),
+lfq_power_t_test_quantiles_V2(),
 plot_stat_density(),
-plot_stat_violin_median(),
+plot_stat_density_median(),
 plot_stat_violin(),
+plot_stat_violin_median(),
 plot_stdv_vs_mean(),
 pooled_V2(),
 summarize_stats()

 
Other summary: 
-hierarchy_counts_sample(),
 hierarchy_counts(),
+hierarchy_counts_sample(),
 nr_B_in_A_per_sample(),
 summarize_hierarchy()

 
Other utilities: 
diff --git a/reference/LFQData.html b/reference/LFQData.html
index df68c073e..7a4ee599e 100644
--- a/reference/LFQData.html
+++ b/reference/LFQData.html
@@ -560,84 +560,15 @@ 
Arguments
     
Examples

     

-istar <- prolfqua_data('data_ionstar')
-istar$config <- old2new(istar$config)
-data <- istar$data |> dplyr::filter(protein_Id %in% sample(protein_Id, 100))
-lfqdata <- LFQData$new(data, istar$config)
+istar <- sim_lfq_data_peptide_config()
+#> sample already exists
+#> completing cases
+
+lfqdata <- LFQData$new(istar$data, istar$config)
 lfqdata$filter_proteins_by_peptide_count()
 #> removing proteins with less than: 2 peptpides
 #> Column added : nr_peptide_Id_IN_protein_Id
 tmp <- lfqdata$to_wide()
-tmp
-#> $data
-#> # A tibble: 838 × 23
-#>    protein_Id       peptide_Id isotope `a~10` `a~11` `a~20` `a~21` `b~02` `b~09`
-#>    <chr>            <chr>      <chr>    <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>
-#>  1 CON__P02769~18~… AEFVEVTK   light   3.29e8 6.06e8 6.07e8 5.72e8 2.98e8 4.48e8
-#>  2 CON__P02769~18~… DDPHACYST… light   1.81e8 2.33e8 2.31e8 2.27e8 1.86e8 1.74e8
-#>  3 CON__P02769~18~… DDPHACYST… light   3.40e7 4.62e7 4.91e7 4.83e7 3.31e7 2.98e7
-#>  4 CON__P02769~18~… ECCHGDLLE… light   8.05e6 1.30e7 1.48e7 1.27e7 1.12e7 9.86e6
-#>  5 CON__P02769~18~… ETYGDMADC… light   1.18e7 3.99e7 2.24e7 2.54e7 2.17e7 1.23e7
-#>  6 CON__P02769~18~… EYEATLEEC… light   1.64e7 3.08e7 2.86e7 3.17e7 1.95e7 1.53e7
-#>  7 CON__P02769~18~… FKDLGEEHFK light   8.31e8 1.18e9 1.45e9 1.62e9 9.71e8 9.16e8
-#>  8 CON__P02769~18~… HLVDEPQNL… light   1.91e9 2.20e9 2.35e9 2.32e9 2.08e9 1.78e9
-#>  9 CON__P02769~18~… HPEYAVSVL… light   4.41e7 6.28e7 4.71e7 6.38e7 4.90e7 6.99e7
-#> 10 CON__P02769~18~… HPYFYAPEL… light   1.43e8 2.26e8 2.10e8 1.84e8 1.84e8 1.70e8
-#> # ℹ 828 more rows
-#> # ℹ 14 more variables: `b~12` <dbl>, `b~19` <dbl>, `c~03` <dbl>, `c~08` <dbl>,
-#> #   `c~13` <dbl>, `c~18` <dbl>, `d~04` <dbl>, `d~07` <dbl>, `d~14` <dbl>,
-#> #   `d~17` <dbl>, `e~05` <dbl>, `e~06` <dbl>, `e~15` <dbl>, `e~16` <dbl>
-#> 
-#> $annotation
-#> # A tibble: 20 × 5
-#>    sampleName raw.file                                  dilution. run_Id isotope
-#>    <chr>      <chr>                                     <chr>     <chr>  <chr>  
-#>  1 a~10       b03_10_150304_human_ecoli_a_3ul_3um_colu… a         10     light  
-#>  2 a~11       b03_11_150304_human_ecoli_a_3ul_3um_colu… a         11     light  
-#>  3 a~20       b03_20_150304_human_ecoli_a_3ul_3um_colu… a         20     light  
-#>  4 a~21       b03_21_150304_human_ecoli_a_3ul_3um_colu… a         21     light  
-#>  5 b~02       b03_02_150304_human_ecoli_b_3ul_3um_colu… b         02     light  
-#>  6 b~09       b03_09_150304_human_ecoli_b_3ul_3um_colu… b         09     light  
-#>  7 b~12       b03_12_150304_human_ecoli_b_3ul_3um_colu… b         12     light  
-#>  8 b~19       b03_19_150304_human_ecoli_b_3ul_3um_colu… b         19     light  
-#>  9 c~03       b03_03_150304_human_ecoli_c_3ul_3um_colu… c         03     light  
-#> 10 c~08       b03_08_150304_human_ecoli_c_3ul_3um_colu… c         08     light  
-#> 11 c~13       b03_13_150304_human_ecoli_c_3ul_3um_colu… c         13     light  
-#> 12 c~18       b03_18_150304_human_ecoli_c_3ul_3um_colu… c         18     light  
-#> 13 d~04       b03_04_150304_human_ecoli_d_3ul_3um_colu… d         04     light  
-#> 14 d~07       b03_07_150304_human_ecoli_d_3ul_3um_colu… d         07     light  
-#> 15 d~14       b03_14_150304_human_ecoli_d_3ul_3um_colu… d         14     light  
-#> 16 d~17       b03_17_150304_human_ecoli_d_3ul_3um_colu… d         17     light  
-#> 17 e~05       b03_05_150304_human_ecoli_e_3ul_3um_colu… e         05     light  
-#> 18 e~06       b03_06_150304_human_ecoli_e_3ul_3um_colu… e         06     light  
-#> 19 e~15       b03_15_150304_human_ecoli_e_3ul_3um_colu… e         15     light  
-#> 20 e~16       b03_16_150304_human_ecoli_e_3ul_3um_colu… e         16     light  
-#> 
-#> $rowdata
-#> # A tibble: 838 × 3
-#>    protein_Id        peptide_Id          isotope
-#>    <chr>             <chr>               <chr>  
-#>  1 CON__P02769~18~NA AEFVEVTK            light  
-#>  2 CON__P02769~18~NA DDPHACYSTVFDK       light  
-#>  3 CON__P02769~18~NA DDPHACYSTVFDKLK     light  
-#>  4 CON__P02769~18~NA ECCHGDLLECADDRADLAK light  
-#>  5 CON__P02769~18~NA ETYGDMADCCEK        light  
-#>  6 CON__P02769~18~NA EYEATLEECCAK        light  
-#>  7 CON__P02769~18~NA FKDLGEEHFK          light  
-#>  8 CON__P02769~18~NA HLVDEPQNLIK         light  
-#>  9 CON__P02769~18~NA HPEYAVSVLLR         light  
-#> 10 CON__P02769~18~NA HPYFYAPELLYYANK     light  
-#> # ℹ 828 more rows
-#> 
-#> $config
-#> <AnalysisConfiguration>
-#>   Public:
-#>     clone: function (deep = FALSE) 
-#>     initialize: function (analysisTableAnnotation, analysisParameter = AnalysisParameters$new()) 
-#>     parameter: AnalysisParameters, R6
-#>     sep: ~
-#>     table: AnalysisTableAnnotation, R6
-#> 
 testthat::expect_equal(nrow(tmp$data) , nrow(tmp$rowdata))
 testthat::expect_equal(ncol(tmp$data) , nrow(tmp$annotation) + ncol(tmp$rowdata))
 
@@ -646,7 +577,7 @@ 
Examples

 stopifnot("matrix" %in% class(tmp$data))
 stopifnot(lfqdata$is_transformed()==FALSE)
 dim(lfqdata$summarize_hierarchy())
-#> [1] 66  3
+#> [1] 6 3
 
 # filter for missing values
 f1 <- lfqdata$omit_NA(nrNA = 0)
@@ -660,12 +591,10 @@ 
Examples

 stopifnot(f2$hierarchy_counts() <= lfqdata$hierarchy_counts())
 
 lfqdata$response()
-#> [1] "peptide.intensity"
+#> [1] "abundance"
 lfqdata$rename_response("peptide.intensity")
-#> peptide.intensity  already in data : protein_Id raw.file sampleName dilution. run_Id isotope peptide_Id peptide.intensity pep nr_peptide_Id_IN_protein_Id .
 lfqdata$response()
 #> [1] "peptide.intensity"
-lfqdata$get_Plotter()$heatmap()
 stopifnot("LFQData" %in% class(lfqdata$get_copy()))
 stopifnot("LFQDataTransformer" %in% class(lfqdata$get_Transformer()))
 stopifnot("LFQDataStats" %in% class(lfqdata$get_Stats()))
@@ -677,13 +606,14 @@ 
Examples

 stopifnot("LFQDataAggregator" %in% class(lfqdata$get_Aggregator()))
 
 lfqdata2 <- lfqdata$get_copy()
-lfqdata2$data <- lfqdata2$data[1:500,]
+lfqdata2$data <- lfqdata2$data[1:100,]
 res <- lfqdata$filter_difference(lfqdata2)
-stopifnot(nrow(res$data) == nrow(lfqdata$data) - 500)
-tmp <- lfqdata$get_sample(40, seed = 4)
-#> Sampling 40protein_Id
+stopifnot(nrow(res$data) == nrow(lfqdata$data) - 100)
+
+tmp <- lfqdata$get_sample(5, seed = 4)
+#> Sampling 5protein_Id
 #> Joining with `by = join_by(protein_Id)`
-stopifnot(nrow(tmp$hierarchy()) == 40)
+stopifnot(nrow(tmp$hierarchy()) == 5)
 
 lw <- lfqdata$get_Writer()
 stopifnot(names(lw$get_wide()) %in% c("data", "annotation"))
diff --git a/reference/LFQDataAggregator-1.png b/reference/LFQDataAggregator-1.png
index 1e5c9b033..4ab2f4137 100644
Binary files a/reference/LFQDataAggregator-1.png and b/reference/LFQDataAggregator-1.png differ
diff --git a/reference/LFQDataAggregator-2.png b/reference/LFQDataAggregator-2.png
index 28ac3d042..3aa650929 100644
Binary files a/reference/LFQDataAggregator-2.png and b/reference/LFQDataAggregator-2.png differ
diff --git a/reference/LFQDataAggregator.html b/reference/LFQDataAggregator.html
index e964b7b68..d19091d4d 100644
--- a/reference/LFQDataAggregator.html
+++ b/reference/LFQDataAggregator.html
@@ -102,12 +102,12 @@ 
Decorates LFQData with methods to aggregate protein intensities
     
     

@@ -331,7 +331,7 @@ 
Examples

 #> Column added : log2_peptide.intensity
 lfqTrans <- lfqTrans$robscale()$lfq
 #> data is : TRUE
-#> Warning: Expected 2 pieces. Additional pieces discarded in 14080 rows [1, 2, 3, 4, 5, 6,
+#> Warning: Expected 2 pieces. Additional pieces discarded in 14400 rows [1, 2, 3, 4, 5, 6,
 #> 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
 #> Joining with `by = join_by(protein_Id, sampleName, peptide_Id)`
 lfqAggregator <- LFQDataAggregator$new(lfqTrans, "protein")
@@ -341,8 +341,10 @@ 
Examples

 #> Warning: medpolish() did not converge in 10 iterations
 pmed <- lfqAggregator$plot()
 pmed$plots[[2]]
-#> Warning: Removed 4 rows containing missing values (`geom_point()`).
-#> Warning: Removed 1 row containing missing values (`geom_line()`).
+#> Warning: Removed 4 rows containing missing values or values outside the scale range
+#> (`geom_point()`).
+#> Warning: Removed 1 row containing missing values or values outside the scale range
+#> (`geom_line()`).
 
 lfqAggregator$lmrob()
 #> starting aggregation
@@ -351,10 +353,14 @@ 
Examples

 #> Warning: 'rlm' failed to converge in 20 steps
 #> Warning: 'rlm' failed to converge in 20 steps
 #> Warning: 'rlm' failed to converge in 20 steps
+#> Warning: 'rlm' failed to converge in 20 steps
+#> Warning: 'rlm' failed to converge in 20 steps
 prob <- lfqAggregator$plot()
 prob$plots[[2]]
-#> Warning: Removed 4 rows containing missing values (`geom_point()`).
-#> Warning: Removed 1 row containing missing values (`geom_line()`).
+#> Warning: Removed 4 rows containing missing values or values outside the scale range
+#> (`geom_point()`).
+#> Warning: Removed 1 row containing missing values or values outside the scale range
+#> (`geom_line()`).
 
 
 lfqCopy <- lfqdata$clone()
@@ -366,8 +372,10 @@ 
Examples

 #> Columns added : srm_meanInt srm_meanIntRank
 pSum <- lfqAggregator$plot()
 pSum$plots[[2]]
-#> Warning: Removed 4 rows containing missing values (`geom_point()`).
-#> Warning: Removed 1 row containing missing values (`geom_line()`).
+#> Warning: Removed 4 rows containing missing values or values outside the scale range
+#> (`geom_point()`).
+#> Warning: Removed 1 row containing missing values or values outside the scale range
+#> (`geom_line()`).
 
 
 lfqAggregator$mean_topN()
@@ -375,8 +383,10 @@ 
Examples

 #> Columns added : srm_meanInt srm_meanIntRank
 pMean <- lfqAggregator$plot()
 pMean$plots[[2]]
-#> Warning: Removed 4 rows containing missing values (`geom_point()`).
-#> Warning: Removed 1 row containing missing values (`geom_line()`).
+#> Warning: Removed 4 rows containing missing values or values outside the scale range
+#> (`geom_point()`).
+#> Warning: Removed 1 row containing missing values or values outside the scale range
+#> (`geom_line()`).
 
 # lfqAggregator$write_plots(".")
 protPlotter <- lfqAggregator$lfq_agg$get_Plotter()
diff --git a/reference/LFQDataPlotter.html b/reference/LFQDataPlotter.html
index a10f05757..bd578b1d5 100644
--- a/reference/LFQDataPlotter.html
+++ b/reference/LFQDataPlotter.html
@@ -104,12 +104,12 @@ 
See also

     
plot_heatmap_cor

 
plot_pca

 
Other LFQData: 
+LFQData,
 LFQDataAggregator,
 LFQDataStats,
 LFQDataSummariser,
 LFQDataToSummarizedExperiment(),
 LFQDataWriter,
-LFQData,
 ProteinAnnotation

     

     

@@ -307,9 +307,17 @@ 
ReturnsMethod boxplots()

 
boxplots for all proteins

 
Usage

-
LFQDataPlotter$boxplots()

+
LFQDataPlotter$boxplots(facet = TRUE)

 

 
+

+
Arguments

+
facet

+
enable facet wrap if hierarchy_depth less then hierarchy lenght.

+
+
+

+

 

 
Returns

 
tibble with column boxplots containing ggplot objects

@@ -347,7 +355,7 @@ 
Usage
 

 
 

-
Arguments

+
Arguments

 
legend

 
show legend TRUE, FALSE do not show.

 
@@ -379,7 +387,7 @@ 
Usage
 
 

-
Arguments

+
Arguments

 
max

 
maximal number of samples to show

 
@@ -419,15 +427,19 @@ 
ReturnsMethod write_boxplots()

 
write boxplots to file

 
Usage

-
LFQDataPlotter$write_boxplots(path_qc, width = 6, height = 6)

+
LFQDataPlotter$write_boxplots(path_qc, filename = NULL, width = 6, height = 6)

 

 
 

-
Arguments

+
Arguments

 
path_qc

 
path to write to

 
 
+
filename

+
file to write into

+
+
 
width

 
fig width

 
@@ -447,7 +459,7 @@ 
Usage
 
 

-
Arguments

+
Arguments

 
fig

 
pltly figure

 
@@ -475,7 +487,7 @@ 
Usage
 
 

-
Arguments

+
Arguments

 
fig

 
ggplot or pheatmap

 
@@ -511,7 +523,7 @@ 
Usage
 
 

-
Arguments

+
Arguments

 
path_qc

 
path to write to

 
@@ -527,7 +539,7 @@ 
Usage
 
 

-
Arguments

+
Arguments

 
deep

 
Whether to make a deep clone.

 
@@ -549,8 +561,9 @@ 
Examples

 lfqdata <- LFQData$new(
  istar$data,
  istar$config)
-#LFQDataPlotter$debug("pca_plotly")
+#LFQDataPlotter$debug("boxplots")
 lfqplotter <- lfqdata$get_Plotter()
+
 stopifnot(class(lfqplotter$heatmap()) == "pheatmap")
 stopifnot(class(lfqplotter$heatmap_cor()) == "pheatmap")
 stopifnot("ggplot" %in% class(lfqplotter$pca()))
diff --git a/reference/LFQDataStats-1.png b/reference/LFQDataStats-1.png
index 55c22bbf5..0afd28d57 100644
Binary files a/reference/LFQDataStats-1.png and b/reference/LFQDataStats-1.png differ
diff --git a/reference/LFQDataStats.html b/reference/LFQDataStats.html
index 92d302c63..1f4a057c3 100644
--- a/reference/LFQDataStats.html
+++ b/reference/LFQDataStats.html
@@ -99,12 +99,12 @@ 
Details

     
     

@@ -422,8 +422,10 @@ 
Examples

 #> #   mean_c <dbl>, mean_d <dbl>, mean_e <dbl>, mean_All <dbl>, CV_a <dbl>,
 #> #   CV_b <dbl>, CV_c <dbl>, CV_d <dbl>, CV_e <dbl>, CV_All <dbl>
 lfqstats$violin()
-#> Warning: Removed 428 rows containing non-finite values (`stat_ydensity()`).
-#> Warning: Removed 428 rows containing non-finite values (`stat_summary()`).
+#> Warning: Removed 428 rows containing non-finite outside the scale range
+#> (`stat_ydensity()`).
+#> Warning: Removed 428 rows containing non-finite outside the scale range
+#> (`stat_summary()`).
 
 runallfuncs(lfqstats)
 #> Warning: data is not transformed - aborting
diff --git a/reference/LFQDataSummariser-4.png b/reference/LFQDataSummariser-4.png
index 455a19fd8..6bad01db0 100644
Binary files a/reference/LFQDataSummariser-4.png and b/reference/LFQDataSummariser-4.png differ
diff --git a/reference/LFQDataSummariser.html b/reference/LFQDataSummariser.html
index bcda3fdc7..99d68df50 100644
--- a/reference/LFQDataSummariser.html
+++ b/reference/LFQDataSummariser.html
@@ -95,12 +95,12 @@ 
Summarize LFQData

     
     

diff --git a/reference/LFQDataToSummarizedExperiment.html b/reference/LFQDataToSummarizedExperiment.html
index 038a1c360..03cfd51c1 100644
--- a/reference/LFQDataToSummarizedExperiment.html
+++ b/reference/LFQDataToSummarizedExperiment.html
@@ -108,12 +108,12 @@ 
Value

     
 
diff --git a/reference/LFQDataTransformer-1.png b/reference/LFQDataTransformer-1.png
index eb9952e39..a86c0b3a3 100644
Binary files a/reference/LFQDataTransformer-1.png and b/reference/LFQDataTransformer-1.png differ
diff --git a/reference/LFQDataTransformer-2.png b/reference/LFQDataTransformer-2.png
index eb9952e39..a86c0b3a3 100644
Binary files a/reference/LFQDataTransformer-2.png and b/reference/LFQDataTransformer-2.png differ
diff --git a/reference/LFQDataTransformer-3.png b/reference/LFQDataTransformer-3.png
new file mode 100644
index 000000000..931361c6c
Binary files /dev/null and b/reference/LFQDataTransformer-3.png differ
diff --git a/reference/LFQDataTransformer.html b/reference/LFQDataTransformer.html
index 51faee999..bfabbce03 100644
--- a/reference/LFQDataTransformer.html
+++ b/reference/LFQDataTransformer.html
@@ -393,7 +393,18 @@ 
Examples

 #>     e~05     e~06     e~15     e~16 
 #> 2.292379 2.265091 2.231205 2.212036 
 #> 
-
+if(require("preprocessCore")){
+quant <- function(y){
+ ynorm <- preprocessCore::normalize.quantiles(y)
+ rownames(ynorm) <- rownames(y)
+ colnames(ynorm) <- colnames(y)
+ return(ynorm)
+}
+ res <- lfqTrans$intensity_matrix( .func = quant)
+ res$lfq$get_Plotter()$intensity_distribution_density()
+}
+#> Warning: data already transformed. If you still want to log2 tranform, set force = TRUE
+
 
 

     

diff --git a/reference/LFQDataWriter.html b/reference/LFQDataWriter.html
index 176ae9838..f5c2bddda 100644
--- a/reference/LFQDataWriter.html
+++ b/reference/LFQDataWriter.html
@@ -96,12 +96,12 @@ 
Write LFQData, or provide outputs for writing.

     
See also

     
LFQData

 
Other LFQData: 
+LFQData,
 LFQDataAggregator,
 LFQDataPlotter,
 LFQDataStats,
 LFQDataSummariser,
 LFQDataToSummarizedExperiment(),
-LFQData,
 ProteinAnnotation

     

     

diff --git a/reference/LR_test.html b/reference/LR_test.html
index dedd1614a..5c10bd577 100644
--- a/reference/LR_test.html
+++ b/reference/LR_test.html
@@ -129,14 +129,13 @@ 
Arguments

     

     
See also

     
Other modelling: 
+Contrasts,
 ContrastsMissing,
 ContrastsModerated,
 ContrastsPlotter,
 ContrastsProDA,
 ContrastsROPECA,
-ContrastsSAINTexpress,
 ContrastsTable,
-Contrasts,
 INTERNAL_FUNCTIONS_BY_FAMILY,
 Model,
 build_model(),
@@ -153,12 +152,12 @@ 
See also

 merge_contrasts_results(),
 model_analyse(),
 model_summary(),
-moderated_p_limma_long(),
 moderated_p_limma(),
+moderated_p_limma_long(),
 my_contest(),
+my_contrast(),
 my_contrast_V1(),
 my_contrast_V2(),
-my_contrast(),
 my_glht(),
 pivot_model_contrasts_2_Wide(),
 plot_lmer_model_and_data(),
diff --git a/reference/Model-2.png b/reference/Model-2.png
index 031f6220c..02fc568a4 100644
Binary files a/reference/Model-2.png and b/reference/Model-2.png differ
diff --git a/reference/Model.html b/reference/Model.html
index 52b80e44a..82ecc7973 100644
--- a/reference/Model.html
+++ b/reference/Model.html
@@ -95,14 +95,13 @@ 
R6 class representing modelling result

     

     
See also

     
Other modelling: 
+Contrasts,
 ContrastsMissing,
 ContrastsModerated,
 ContrastsPlotter,
 ContrastsProDA,
 ContrastsROPECA,
-ContrastsSAINTexpress,
 ContrastsTable,
-Contrasts,
 INTERNAL_FUNCTIONS_BY_FAMILY,
 LR_test(),
 build_model(),
@@ -119,12 +118,12 @@ 
See also

 merge_contrasts_results(),
 model_analyse(),
 model_summary(),
-moderated_p_limma_long(),
 moderated_p_limma(),
+moderated_p_limma_long(),
 my_contest(),
+my_contrast(),
 my_contrast_V1(),
 my_contrast_V2(),
-my_contrast(),
 my_glht(),
 pivot_model_contrasts_2_Wide(),
 plot_lmer_model_and_data(),
diff --git a/reference/PACKAGE_DATA.html b/reference/PACKAGE_DATA.html
index 04a9fcf50..0b40b1216 100644
--- a/reference/PACKAGE_DATA.html
+++ b/reference/PACKAGE_DATA.html
@@ -99,8 +99,8 @@ 
See also

 data_basicModel_p1807,
 data_benchmarkExample,
 data_checksummarizationrobust87,
-data_checksummarizerobust69,
 data_checksummarizerobust,
+data_checksummarizerobust69,
 data_correlatedPeptideList,
 data_factor_levelContrasts,
 data_interactionModel_p1807,
diff --git a/reference/ProteinAnnotation.html b/reference/ProteinAnnotation.html
index 9cfa8cc81..0d32219d0 100644
--- a/reference/ProteinAnnotation.html
+++ b/reference/ProteinAnnotation.html
@@ -95,13 +95,13 @@ 
Decorates LFQData with a row annotation and some protein specific functions.
     
     

     

     
Public fields

diff --git a/reference/UpSet_interaction_missing_stats.html b/reference/UpSet_interaction_missing_stats.html
index 89c034466..7a63bdc25 100644
--- a/reference/UpSet_interaction_missing_stats.html
+++ b/reference/UpSet_interaction_missing_stats.html
@@ -107,16 +107,16 @@ 
See also

 UpSet_missing_stats(),
 medpolish_estimate_df(),
 missigness_histogram(),
-missingness_per_condition_cumsum(),
 missingness_per_condition(),
+missingness_per_condition_cumsum(),
 plot_NA_heatmap(),
 plot_estimate(),
-plot_heatmap_cor(),
 plot_heatmap(),
+plot_heatmap_cor(),
 plot_hierarchies_add_quantline(),
 plot_hierarchies_boxplot_df(),
-plot_hierarchies_line_df(),
 plot_hierarchies_line(),
+plot_hierarchies_line_df(),
 plot_intensity_distribution_violin(),
 plot_pca(),
 plot_raster(),
@@ -128,8 +128,8 @@ 
See also

 get_contrast(),
 missigness_histogram(),
 missigness_impute_factors_interactions(),
-missingness_per_condition_cumsum(),
-missingness_per_condition()

+missingness_per_condition(),
+missingness_per_condition_cumsum()

     

 
     

diff --git a/reference/UpSet_missing_stats.html b/reference/UpSet_missing_stats.html
index f5ab77d4a..8eced4e5d 100644
--- a/reference/UpSet_missing_stats.html
+++ b/reference/UpSet_missing_stats.html
@@ -101,16 +101,16 @@ 
See also

 UpSet_interaction_missing_stats(),
 medpolish_estimate_df(),
 missigness_histogram(),
-missingness_per_condition_cumsum(),
 missingness_per_condition(),
+missingness_per_condition_cumsum(),
 plot_NA_heatmap(),
 plot_estimate(),
-plot_heatmap_cor(),
 plot_heatmap(),
+plot_heatmap_cor(),
 plot_hierarchies_add_quantline(),
 plot_hierarchies_boxplot_df(),
-plot_hierarchies_line_df(),
 plot_hierarchies_line(),
+plot_hierarchies_line_df(),
 plot_intensity_distribution_violin(),
 plot_pca(),
 plot_raster(),
@@ -122,8 +122,8 @@ 
See also

 get_contrast(),
 missigness_histogram(),
 missigness_impute_factors_interactions(),
-missingness_per_condition_cumsum(),
-missingness_per_condition()

+missingness_per_condition(),
+missingness_per_condition_cumsum()

     

 
     

diff --git a/reference/aggregate_contrast.html b/reference/aggregate_contrast.html
index 3579d115c..c5f88539c 100644
--- a/reference/aggregate_contrast.html
+++ b/reference/aggregate_contrast.html
@@ -111,8 +111,8 @@ 
See also

 get_contrast(),
 missigness_histogram(),
 missigness_impute_factors_interactions(),
-missingness_per_condition_cumsum(),
-missingness_per_condition()

+missingness_per_condition(),
+missingness_per_condition_cumsum()
diff --git a/reference/aggregate_intensity_topN.html b/reference/aggregate_intensity_topN.html index 2c56a4a6c..2d068237d 100644 --- a/reference/aggregate_intensity_topN.html +++ b/reference/aggregate_intensity_topN.html @@ -123,16 +123,16 @@

See also

INTERNAL_FUNCTIONS_BY_FAMILY, estimate_intensity(), intensity_summary_by_hkeys(), -medpolish_estimate_dfconfig(), -medpolish_estimate_df(), medpolish_estimate(), +medpolish_estimate_df(), +medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), -plot_hierarchies_line_df(), plot_hierarchies_line(), -rlm_estimate_dfconfig(), -rlm_estimate()

+plot_hierarchies_line_df(), +rlm_estimate(), +rlm_estimate_dfconfig()

diff --git a/reference/apply_to_response_matrix.html b/reference/apply_to_response_matrix.html index 64ef2179f..b2bef14cd 100644 --- a/reference/apply_to_response_matrix.html +++ b/reference/apply_to_response_matrix.html @@ -119,8 +119,8 @@

See also

get_robscales(), normalize_log2_robscale(), robust_scale(), -scale_with_subset_by_factors(), -scale_with_subset()

+scale_with_subset(), +scale_with_subset_by_factors()

diff --git a/reference/build_model.html b/reference/build_model.html index 2dda6823c..746b06de4 100644 --- a/reference/build_model.html +++ b/reference/build_model.html @@ -133,14 +133,13 @@

Value

See also

model_analyse, strategy_lmer strategy_lm

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -157,12 +156,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/contrasts_fisher_exact.html b/reference/contrasts_fisher_exact.html index 084f57fa6..eb85ca564 100644 --- a/reference/contrasts_fisher_exact.html +++ b/reference/contrasts_fisher_exact.html @@ -102,14 +102,13 @@

Fishers exact test on a datframe

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -126,12 +125,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/copy_SAINTe_doc.html b/reference/copy_SAINTe_doc.html index f2af61626..fd3a4da13 100644 --- a/reference/copy_SAINTe_doc.html +++ b/reference/copy_SAINTe_doc.html @@ -103,9 +103,11 @@

Arguments

Examples

copy_SAINTe_doc(workdir = tempdir())
-#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/SaintExpress/SAINTexpress-manual.docx to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/SAINTexpress-manual.docx
-#> your working directory now should contain:  1 new files :
-#> [1] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/SAINTexpress-manual.docx"
+#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/SaintExpress/SAINTexpress-manual.docx to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/SAINTexpress-manual.docx
+#> Warning: could not copy script file. /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/SAINTexpress-manual.docx
+#> Warning: could not copy script file. /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/inst/SaintExpress/SAINTexpress-manual.docx  to  /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/SAINTexpress-manual.docx
+#> your working directory now should contain:  0 new files :
+#> NULL
diff --git a/reference/copy_mixed_model_analysis_script.html b/reference/copy_mixed_model_analysis_script.html index 1101f7d02..27d1478c8 100644 --- a/reference/copy_mixed_model_analysis_script.html +++ b/reference/copy_mixed_model_analysis_script.html @@ -103,19 +103,19 @@

Arguments

Examples

copy_mixed_model_analysis_script(workdir = tempdir())
-#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/fgcz_formatting/fgcz_header.html to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/fgcz_header.html
-#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/fgcz_formatting/fgcz_footer.html to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/fgcz_footer.html
-#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/fgcz_formatting/fgcz.css to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/fgcz.css
-#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/fgcz_formatting/fgcz_banner.png to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/fgcz_banner.png
-#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/rmarkdown/mixed_model_analysis_script_Report.Rmd to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/mixed_model_analysis_script_Report.Rmd
-#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/rmarkdown/bibliography.bib to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/bibliography.bib
+#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/fgcz_formatting/fgcz_header.html to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/fgcz_header.html
+#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/fgcz_formatting/fgcz_footer.html to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/fgcz_footer.html
+#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/fgcz_formatting/fgcz.css to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/fgcz.css
+#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/fgcz_formatting/fgcz_banner.png to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/fgcz_banner.png
+#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/rmarkdown/mixed_model_analysis_script_Report.Rmd to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/mixed_model_analysis_script_Report.Rmd
+#> copy /Users/witoldwolski/__checkout/proLFQuaPackageBuildScripts/test_build_prolfqua/prolfqua/rmarkdown/bibliography.bib to /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/bibliography.bib
 #> your working directory now should contain:  6 new files :
-#> [1] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/fgcz_header.html"                      
-#> [2] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/fgcz_footer.html"                      
-#> [3] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/fgcz.css"                              
-#> [4] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/fgcz_banner.png"                       
-#> [5] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/mixed_model_analysis_script_Report.Rmd"
-#> [6] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/bibliography.bib"                      
+#> [1] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/fgcz_header.html"                      
+#> [2] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/fgcz_footer.html"                      
+#> [3] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/fgcz.css"                              
+#> [4] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/fgcz_banner.png"                       
+#> [5] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/mixed_model_analysis_script_Report.Rmd"
+#> [6] "/var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//Rtmp6NIwVm/bibliography.bib"
diff --git a/reference/cor_jackknife_matrix.html b/reference/cor_jackknife_matrix.html index 9017be8e1..134956960 100644 --- a/reference/cor_jackknife_matrix.html +++ b/reference/cor_jackknife_matrix.html @@ -109,8 +109,8 @@

Arguments

See also

Other transitioncorrlation: cor_order(), -jackknife_matrix(), -jackknife()

+jackknife(), +jackknife_matrix()

diff --git a/reference/cor_order.html b/reference/cor_order.html index e8c1b97e1..3377b94c5 100644 --- a/reference/cor_order.html +++ b/reference/cor_order.html @@ -103,8 +103,8 @@

Arguments

See also

Other transitioncorrlation: cor_jackknife_matrix(), -jackknife_matrix(), -jackknife()

+jackknife(), +jackknife_matrix()

diff --git a/reference/data_IonstarProtein_subsetNorm.html b/reference/data_IonstarProtein_subsetNorm.html index 3ad56ac6a..a2f2f0aaf 100644 --- a/reference/data_IonstarProtein_subsetNorm.html +++ b/reference/data_IonstarProtein_subsetNorm.html @@ -106,8 +106,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_SAINTe_output.html b/reference/data_SAINTe_output.html index 6fb290c7e..164dc6c38 100644 --- a/reference/data_SAINTe_output.html +++ b/reference/data_SAINTe_output.html @@ -88,7 +88,7 @@

SAINT express output

SAINT express output produced by running the function -runSaint

+runSaint

@@ -101,7 +101,7 @@

Format

See also

-

runSaint

+

runSaint

Other data: PACKAGE_DATA, data_IonstarProtein_subsetNorm, @@ -109,8 +109,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_Yeast2Factor.html b/reference/data_Yeast2Factor.html index 104385198..dcff1d9e2 100644 --- a/reference/data_Yeast2Factor.html +++ b/reference/data_Yeast2Factor.html @@ -106,8 +106,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_basicModel_p1807.html b/reference/data_basicModel_p1807.html index 7cd52dd87..ab5e0a7e6 100644 --- a/reference/data_basicModel_p1807.html +++ b/reference/data_basicModel_p1807.html @@ -106,8 +106,8 @@

See also

data_Yeast2Factor, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_benchmarkExample.html b/reference/data_benchmarkExample.html index 861bb472e..1be6a4c1e 100644 --- a/reference/data_benchmarkExample.html +++ b/reference/data_benchmarkExample.html @@ -106,8 +106,8 @@

See also

data_Yeast2Factor, data_basicModel_p1807, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_checksummarizationrobust87.html b/reference/data_checksummarizationrobust87.html index 23b7a5d69..7c8aa1c8d 100644 --- a/reference/data_checksummarizationrobust87.html +++ b/reference/data_checksummarizationrobust87.html @@ -106,8 +106,8 @@

See also

data_Yeast2Factor, data_basicModel_p1807, data_benchmarkExample, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_correlatedPeptideList.html b/reference/data_correlatedPeptideList.html index 3741b99f1..23163a02f 100644 --- a/reference/data_correlatedPeptideList.html +++ b/reference/data_correlatedPeptideList.html @@ -107,8 +107,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_factor_levelContrasts, data_interactionModel_p1807, data_ionstar, diff --git a/reference/data_factor_levelContrasts.html b/reference/data_factor_levelContrasts.html index dc748bc5b..6695cbf27 100644 --- a/reference/data_factor_levelContrasts.html +++ b/reference/data_factor_levelContrasts.html @@ -107,8 +107,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_interactionModel_p1807, data_ionstar, diff --git a/reference/data_interactionModel_p1807.html b/reference/data_interactionModel_p1807.html index 232267e87..2bcb912b2 100644 --- a/reference/data_interactionModel_p1807.html +++ b/reference/data_interactionModel_p1807.html @@ -107,8 +107,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_ionstar, diff --git a/reference/data_ionstar.html b/reference/data_ionstar.html index 02bb7c5d7..fc2521045 100644 --- a/reference/data_ionstar.html +++ b/reference/data_ionstar.html @@ -107,8 +107,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_lm_models_to_test.html b/reference/data_lm_models_to_test.html index 83b8010fb..0d5baf168 100644 --- a/reference/data_lm_models_to_test.html +++ b/reference/data_lm_models_to_test.html @@ -107,8 +107,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_modellingResult_A.html b/reference/data_modellingResult_A.html index e0c525300..54d5a4ff8 100644 --- a/reference/data_modellingResult_A.html +++ b/reference/data_modellingResult_A.html @@ -107,8 +107,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_models_interaction.html b/reference/data_models_interaction.html index 39a002e40..0dc8b7b69 100644 --- a/reference/data_models_interaction.html +++ b/reference/data_models_interaction.html @@ -107,8 +107,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_multigroupFC.html b/reference/data_multigroupFC.html index 3ba598cd9..deabb74c6 100644 --- a/reference/data_multigroupFC.html +++ b/reference/data_multigroupFC.html @@ -107,8 +107,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_skylinePRMSample_A.html b/reference/data_skylinePRMSample_A.html index 925e616d1..af2f2bdd8 100644 --- a/reference/data_skylinePRMSample_A.html +++ b/reference/data_skylinePRMSample_A.html @@ -107,8 +107,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_skylineSRM_HL_A.html b/reference/data_skylineSRM_HL_A.html index 101b48272..3a40b71a6 100644 --- a/reference/data_skylineSRM_HL_A.html +++ b/reference/data_skylineSRM_HL_A.html @@ -107,8 +107,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_spectronautDIA250_A.html b/reference/data_spectronautDIA250_A.html index 90c1155a3..1d39abc32 100644 --- a/reference/data_spectronautDIA250_A.html +++ b/reference/data_spectronautDIA250_A.html @@ -107,8 +107,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/data_test_confusion_matrix_scores.html b/reference/data_test_confusion_matrix_scores.html index 5a66bcf8b..37b5e9cc0 100644 --- a/reference/data_test_confusion_matrix_scores.html +++ b/reference/data_test_confusion_matrix_scores.html @@ -107,8 +107,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/estimate_intensity.html b/reference/estimate_intensity.html index ad287ed95..e8945635a 100644 --- a/reference/estimate_intensity.html +++ b/reference/estimate_intensity.html @@ -112,16 +112,16 @@

See also

INTERNAL_FUNCTIONS_BY_FAMILY, aggregate_intensity_topN(), intensity_summary_by_hkeys(), -medpolish_estimate_dfconfig(), -medpolish_estimate_df(), medpolish_estimate(), +medpolish_estimate_df(), +medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), -plot_hierarchies_line_df(), plot_hierarchies_line(), -rlm_estimate_dfconfig(), -rlm_estimate()

+plot_hierarchies_line_df(), +rlm_estimate(), +rlm_estimate_dfconfig()

diff --git a/reference/filter_proteins_by_peptide_count.html b/reference/filter_proteins_by_peptide_count.html index 4229b7976..40216134b 100644 --- a/reference/filter_proteins_by_peptide_count.html +++ b/reference/filter_proteins_by_peptide_count.html @@ -117,8 +117,8 @@

See also

get_robscales(), normalize_log2_robscale(), robust_scale(), -scale_with_subset_by_factors(), -scale_with_subset()

+scale_with_subset(), +scale_with_subset_by_factors()

diff --git a/reference/get_anova_df.html b/reference/get_anova_df.html index 0d4445e37..5c7feb850 100644 --- a/reference/get_anova_df.html +++ b/reference/get_anova_df.html @@ -96,14 +96,13 @@

anova returning dataframe

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -120,12 +119,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/get_complete_model_fit.html b/reference/get_complete_model_fit.html index a756960d6..b352fbaf4 100644 --- a/reference/get_complete_model_fit.html +++ b/reference/get_complete_model_fit.html @@ -96,14 +96,13 @@

retrieve complete model.

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -120,12 +119,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/get_contrast.html b/reference/get_contrast.html index 15d5ae695..c1dea4b21 100644 --- a/reference/get_contrast.html +++ b/reference/get_contrast.html @@ -111,8 +111,8 @@

See also

aggregate_contrast(), missigness_histogram(), missigness_impute_factors_interactions(), -missingness_per_condition_cumsum(), -missingness_per_condition()

+missingness_per_condition(), +missingness_per_condition_cumsum()

diff --git a/reference/get_imputed_contrasts.html b/reference/get_imputed_contrasts.html index e5be256eb..fa26a89f6 100644 --- a/reference/get_imputed_contrasts.html +++ b/reference/get_imputed_contrasts.html @@ -122,14 +122,13 @@

Value

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -146,12 +145,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/get_p_values_pbeta.html b/reference/get_p_values_pbeta.html index 0c0aa044d..5b06cfb4c 100644 --- a/reference/get_p_values_pbeta.html +++ b/reference/get_p_values_pbeta.html @@ -102,14 +102,13 @@

Arguments

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -126,12 +125,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/get_robscales.html b/reference/get_robscales.html index bcb5a09c9..6a9c5219a 100644 --- a/reference/get_robscales.html +++ b/reference/get_robscales.html @@ -101,8 +101,8 @@

See also

filter_proteins_by_peptide_count(), normalize_log2_robscale(), robust_scale(), -scale_with_subset_by_factors(), -scale_with_subset()

+scale_with_subset(), +scale_with_subset_by_factors()

diff --git a/reference/index.html b/reference/index.html index 0c4699fd2..6159256b1 100644 --- a/reference/index.html +++ b/reference/index.html @@ -251,10 +251,6 @@

All functions prolfqua_data()

load data from prolfqua

- -

add_protein_lengths() protein_2localSaint() runSaint()

- -

Add protein lengths from fasta file to data frame (id_col - protein id column.)

sim_lfq_data()

diff --git a/reference/intensity_summary_by_hkeys-1.png b/reference/intensity_summary_by_hkeys-1.png index 5ff764483..fb01dbb7a 100644 Binary files a/reference/intensity_summary_by_hkeys-1.png and b/reference/intensity_summary_by_hkeys-1.png differ diff --git a/reference/intensity_summary_by_hkeys.html b/reference/intensity_summary_by_hkeys.html index 4f8ada488..e63d9f7e6 100644 --- a/reference/intensity_summary_by_hkeys.html +++ b/reference/intensity_summary_by_hkeys.html @@ -111,16 +111,16 @@

See also

INTERNAL_FUNCTIONS_BY_FAMILY, aggregate_intensity_topN(), estimate_intensity(), -medpolish_estimate_dfconfig(), -medpolish_estimate_df(), medpolish_estimate(), +medpolish_estimate_df(), +medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), -plot_hierarchies_line_df(), plot_hierarchies_line(), -rlm_estimate_dfconfig(), -rlm_estimate()

+plot_hierarchies_line_df(), +rlm_estimate(), +rlm_estimate_dfconfig()

Other deprecated: INTERNAL_FUNCTIONS_BY_FAMILY, medpolish_protein_estimates(), @@ -157,8 +157,10 @@

Examples

stopifnot(nrow(dd) == length(unique(bb$data$protein_Id))) dd$plot[[2]] -#> Warning: Removed 15 rows containing missing values (`geom_point()`). -#> Warning: Removed 3 rows containing missing values (`geom_point()`). +#> Warning: Removed 15 rows containing missing values or values outside the scale range +#> (`geom_point()`). +#> Warning: Removed 3 rows containing missing values or values outside the scale range +#> (`geom_point()`). # example how to add peptide count information diff --git a/reference/isSingular_lm.html b/reference/isSingular_lm.html index 6698eb425..bc5dd45f9 100644 --- a/reference/isSingular_lm.html +++ b/reference/isSingular_lm.html @@ -96,14 +96,13 @@

check if lm model is singular

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -120,12 +119,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/lfq_power_t_test_proteins.html b/reference/lfq_power_t_test_proteins.html index a49998062..240aa3ea0 100644 --- a/reference/lfq_power_t_test_proteins.html +++ b/reference/lfq_power_t_test_proteins.html @@ -125,12 +125,12 @@

Arguments

See also

Other stats: INTERNAL_FUNCTIONS_BY_FAMILY, -lfq_power_t_test_quantiles_V2(), lfq_power_t_test_quantiles(), -plot_stat_density_median(), +lfq_power_t_test_quantiles_V2(), plot_stat_density(), -plot_stat_violin_median(), +plot_stat_density_median(), plot_stat_violin(), +plot_stat_violin_median(), plot_stdv_vs_mean(), pooled_V2(), summarize_stats()

diff --git a/reference/lfq_power_t_test_quantiles.html b/reference/lfq_power_t_test_quantiles.html index 232d9c0a5..aa6a7f608 100644 --- a/reference/lfq_power_t_test_quantiles.html +++ b/reference/lfq_power_t_test_quantiles.html @@ -128,10 +128,10 @@

See also

INTERNAL_FUNCTIONS_BY_FAMILY, lfq_power_t_test_proteins(), lfq_power_t_test_quantiles_V2(), -plot_stat_density_median(), plot_stat_density(), -plot_stat_violin_median(), +plot_stat_density_median(), plot_stat_violin(), +plot_stat_violin_median(), plot_stdv_vs_mean(), pooled_V2(), summarize_stats()

diff --git a/reference/lfq_power_t_test_quantiles_V2.html b/reference/lfq_power_t_test_quantiles_V2.html index e853fbc3d..7de1fd504 100644 --- a/reference/lfq_power_t_test_quantiles_V2.html +++ b/reference/lfq_power_t_test_quantiles_V2.html @@ -127,10 +127,10 @@

See also

INTERNAL_FUNCTIONS_BY_FAMILY, lfq_power_t_test_proteins(), lfq_power_t_test_quantiles(), -plot_stat_density_median(), plot_stat_density(), -plot_stat_violin_median(), +plot_stat_density_median(), plot_stat_violin(), +plot_stat_violin_median(), plot_stdv_vs_mean(), pooled_V2(), summarize_stats()

diff --git a/reference/linfct_all_possible_contrasts.html b/reference/linfct_all_possible_contrasts.html index f359249d6..91df65e00 100644 --- a/reference/linfct_all_possible_contrasts.html +++ b/reference/linfct_all_possible_contrasts.html @@ -96,14 +96,13 @@

create all possible contrasts

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -120,12 +119,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/linfct_factors_contrasts.html b/reference/linfct_factors_contrasts.html index 314883545..10517944c 100644 --- a/reference/linfct_factors_contrasts.html +++ b/reference/linfct_factors_contrasts.html @@ -96,14 +96,13 @@

create contrasts between factor levels

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -120,12 +119,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/linfct_from_model.html b/reference/linfct_from_model.html index 9858dd0ea..ff9de2e11 100644 --- a/reference/linfct_from_model.html +++ b/reference/linfct_from_model.html @@ -102,14 +102,13 @@

Arguments

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -126,12 +125,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/linfct_matrix_contrasts.html b/reference/linfct_matrix_contrasts.html index 065d706da..3b8171748 100644 --- a/reference/linfct_matrix_contrasts.html +++ b/reference/linfct_matrix_contrasts.html @@ -110,14 +110,13 @@

Arguments

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -134,12 +133,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/mark_decorelated.html b/reference/mark_decorelated.html index 27d31c55c..003815207 100644 --- a/reference/mark_decorelated.html +++ b/reference/mark_decorelated.html @@ -129,7 +129,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 7: `row.names = "ASVHTLSGHTNAVATVR"`, `col.names = +#> ℹ In group 7: `row.names = "ASVHTLSGHTNAVATVR"` and `col.names = #> "VYREDDTATEETHPVSWKPEIIK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -137,7 +137,7 @@

Examples

#> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 2: `row.names = "DVLAHQVPNAK"`, `col.names = +#> ℹ In group 2: `row.names = "DVLAHQVPNAK"` and `col.names = #> "LHTKPSQAPAVEVAPAGASYNPSFEDHQTLLSAAHEVELQR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -145,14 +145,14 @@

Examples

#> Warning: There were 9 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 4: `row.names = "AQLSQYFDAVK"`, `col.names = "FVPTALR"`. +#> ℹ In group 4: `row.names = "AQLSQYFDAVK"` and `col.names = "FVPTALR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 8 remaining warnings. #> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 75: `row.names = "NCPHVVVGTPGR"`, `col.names = +#> ℹ In group 75: `row.names = "NCPHVVVGTPGR"` and `col.names = #> "VNIVFNYDMPEDSDTYLHR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -160,7 +160,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 60: `row.names = "IPELDMTEVVAPFMANIPLLLYPQDGPR"`, `col.names = +#> ℹ In group 60: `row.names = "IPELDMTEVVAPFMANIPLLLYPQDGPR"` and `col.names = #> "TEKEILDAFDK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -168,21 +168,22 @@

Examples

#> Warning: There were 10 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 31: `row.names = "FEAAETLEEAAMR"`, `col.names = "YEEVEYYYQR"`. +#> ℹ In group 31: `row.names = "FEAAETLEEAAMR"` and `col.names = "YEEVEYYYQR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 9 remaining warnings. #> Warning: There were 14 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 5: `row.names = "AIPNQGEILVIR"`, `col.names = "IEGSGDQVDTLELSGGAR"`. +#> ℹ In group 5: `row.names = "AIPNQGEILVIR"` and `col.names = +#> "IEGSGDQVDTLELSGGAR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 13 remaining warnings. #> Warning: There were 268 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 8: `row.names = "AFQQNLVSSALFSK"`, `col.names = +#> ℹ In group 8: `row.names = "AFQQNLVSSALFSK"` and `col.names = #> "HHVLQNDVLAHQSTVEAVNK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -190,21 +191,21 @@

Examples

#> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 30: `row.names = "GDEVIFGEFSWPK"`, `col.names = "SAPLEIGLQR"`. +#> ℹ In group 30: `row.names = "GDEVIFGEFSWPK"` and `col.names = "SAPLEIGLQR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings. #> Warning: There were 33 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 2: `row.names = "DFNPTATVK"`, `col.names = "EGLLFEGR"`. +#> ℹ In group 2: `row.names = "DFNPTATVK"` and `col.names = "EGLLFEGR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 32 remaining warnings. #> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 94: `row.names = "KAEAQIAAK"`, `col.names = +#> ℹ In group 94: `row.names = "KAEAQIAAK"` and `col.names = #> "MNLGVGAYRDDNGKPYVLPSVR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -212,14 +213,14 @@

Examples

#> Warning: There were 67 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 29: `row.names = "AEFVEVTK"`, `col.names = "VHKECCHGDLLECADDR"`. +#> ℹ In group 29: `row.names = "AEFVEVTK"` and `col.names = "VHKECCHGDLLECADDR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 66 remaining warnings. #> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 4: `row.names = "DQQNLPYGVTPASPSGHSQGR"`, `col.names = +#> ℹ In group 4: `row.names = "DQQNLPYGVTPASPSGHSQGR"` and `col.names = #> "TTPTPSTNSVLSTSTNR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -227,7 +228,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 3: `row.names = "LLDGFFIRPFYK"`, `col.names = +#> ℹ In group 3: `row.names = "LLDGFFIRPFYK"` and `col.names = #> "RPTPQDNLTDAENGNIQLQAQR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -235,7 +236,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 8: `row.names = "GVVVQDAALLESGAAIR"`, `col.names = +#> ℹ In group 8: `row.names = "GVVVQDAALLESGAAIR"` and `col.names = #> "TAEGGAEHVQPITGDNIVNVLDDFR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -243,49 +244,50 @@

Examples

#> Warning: There were 19 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 9: `row.names = "ANKLDHVVTIIK"`, `col.names = "VEDLTFTSPFCLQVK"`. +#> ℹ In group 9: `row.names = "ANKLDHVVTIIK"` and `col.names = "VEDLTFTSPFCLQVK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 18 remaining warnings. #> Warning: There were 5 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 3: `row.names = "FALEVPGLR"`, `col.names = "LSETSPAFR"`. +#> ℹ In group 3: `row.names = "FALEVPGLR"` and `col.names = "LSETSPAFR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 4 remaining warnings. #> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 3: `row.names = "MTEWETAAPAVAETPDIK"`, `col.names = "QAVDVSPLRR"`. +#> ℹ In group 3: `row.names = "MTEWETAAPAVAETPDIK"` and `col.names = +#> "QAVDVSPLRR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings. #> Warning: There were 33 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 3: `row.names = "AIEQLKEQAATGK"`, `col.names = "ATIFNLK"`. +#> ℹ In group 3: `row.names = "AIEQLKEQAATGK"` and `col.names = "ATIFNLK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 32 remaining warnings. #> Warning: There were 6 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 2: `row.names = "AAIQSQLDGVR"`, `col.names = "KYVLDDLIVAK"`. +#> ℹ In group 2: `row.names = "AAIQSQLDGVR"` and `col.names = "KYVLDDLIVAK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 5 remaining warnings. #> Warning: There were 11 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 2: `row.names = "ELQHEKDTSSLLR"`, `col.names = "ICSLQEEQQQLR"`. +#> ℹ In group 2: `row.names = "ELQHEKDTSSLLR"` and `col.names = "ICSLQEEQQQLR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 10 remaining warnings. #> Warning: There were 8 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 4: `row.names = "AGQMVTVWAAGAGVAHSPPSTLVWK"`, `col.names = +#> ℹ In group 4: `row.names = "AGQMVTVWAAGAGVAHSPPSTLVWK"` and `col.names = #> "ELEEAMAGERDK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -293,42 +295,44 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 2: `row.names = "AELDLMAPGPLPR"`, `col.names = "VTNTTPWEHPYPDLPSR"`. +#> ℹ In group 2: `row.names = "AELDLMAPGPLPR"` and `col.names = +#> "VTNTTPWEHPYPDLPSR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. #> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 387: `row.names = "GPLEYVPSAK"`, `col.names = "TAVFGFETSEAK"`. +#> ℹ In group 387: `row.names = "GPLEYVPSAK"` and `col.names = "TAVFGFETSEAK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings. #> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 2: `row.names = "EVAWEQNYPDR"`, `col.names = "ITGIDSSPAMIAEAR"`. +#> ℹ In group 2: `row.names = "EVAWEQNYPDR"` and `col.names = "ITGIDSSPAMIAEAR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. #> Warning: There were 6 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 220: `row.names = "VLPLEEAYR"`, `col.names = "VYIGSFWAQPLQNTDNRR"`. +#> ℹ In group 220: `row.names = "VLPLEEAYR"` and `col.names = +#> "VYIGSFWAQPLQNTDNRR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 5 remaining warnings. #> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 121: `row.names = "HIAEDSDRKYEEVAR"`, `col.names = "MELQEMQLK"`. +#> ℹ In group 121: `row.names = "HIAEDSDRKYEEVAR"` and `col.names = "MELQEMQLK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. #> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 7: `row.names = "AQEAPGQAEPPAAAEVQGAGNENEPR"`, `col.names = +#> ℹ In group 7: `row.names = "AQEAPGQAEPPAAAEVQGAGNENEPR"` and `col.names = #> "LLVVDRETDEFFK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -336,7 +340,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 2: `row.names = "AQYVLAEQVTR"`, `col.names = +#> ℹ In group 2: `row.names = "AQYVLAEQVTR"` and `col.names = #> "FQQAGHKPVALVGGATGLIGDPSFK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -344,21 +348,22 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 4: `row.names = "ASAGSYISALR"`, `col.names = "GPGLYYVDEHGTR"`. +#> ℹ In group 4: `row.names = "ASAGSYISALR"` and `col.names = "GPGLYYVDEHGTR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. #> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 146: `row.names = "ETAPGDISPYTIPEEDR"`, `col.names = "PVMQALLHIIR"`. +#> ℹ In group 146: `row.names = "ETAPGDISPYTIPEEDR"` and `col.names = +#> "PVMQALLHIIR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. #> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 3: `row.names = "LKTEEGEIDYSAEEGENRR"`, `col.names = +#> ℹ In group 3: `row.names = "LKTEEGEIDYSAEEGENRR"` and `col.names = #> "TIPGTALVEMGDEYAVER"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -366,7 +371,7 @@

Examples

#> Warning: There were 6 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 27: `row.names = "FSLFAERK"`, `col.names = +#> ℹ In group 27: `row.names = "FSLFAERK"` and `col.names = #> "QLSCVANQNGSQADCELGNPFKR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -374,7 +379,7 @@

Examples

#> Warning: There were 10 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 2: `row.names = "AFAASNELEVNATHKDR"`, `col.names = +#> ℹ In group 2: `row.names = "AFAASNELEVNATHKDR"` and `col.names = #> "EGITATDLVLTVTQMLR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -382,21 +387,21 @@

Examples

#> Warning: There were 7 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 1: `row.names = "AIQAELLK"`, `col.names = "AIQAELLK"`. +#> ℹ In group 1: `row.names = "AIQAELLK"` and `col.names = "AIQAELLK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 6 remaining warnings. #> Warning: There were 16 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 52: `row.names = "EEMLQMIR"`, `col.names = "KANYAVDAYFR"`. +#> ℹ In group 52: `row.names = "EEMLQMIR"` and `col.names = "KANYAVDAYFR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 15 remaining warnings. #> Warning: There were 14 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 577: `row.names = "DHRDNLEFFLAGIGR"`, `col.names = +#> ℹ In group 577: `row.names = "DHRDNLEFFLAGIGR"` and `col.names = #> "FCFTPHTEEGCLSER"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -404,14 +409,14 @@

Examples

#> Warning: There were 3 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 1: `row.names = "FSIALLNQAVER"`, `col.names = "FSIALLNQAVER"`. +#> ℹ In group 1: `row.names = "FSIALLNQAVER"` and `col.names = "FSIALLNQAVER"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 2 remaining warnings. #> Warning: There were 8 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 5: `row.names = "DFYLATSPPDSFLDDHHLTRPHPER"`, `col.names = +#> ℹ In group 5: `row.names = "DFYLATSPPDSFLDDHHLTRPHPER"` and `col.names = #> "NHQDPLAVAYHLIIDNR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -419,14 +424,14 @@

Examples

#> Warning: There were 3 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 2: `row.names = "FIDTSQFILNR"`, `col.names = "SKPVFSESLSD"`. +#> ℹ In group 2: `row.names = "FIDTSQFILNR"` and `col.names = "SKPVFSESLSD"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 2 remaining warnings. #> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 335: `row.names = "EKLCYVALDFEQEMATAASSSSLEK"`, `col.names = +#> ℹ In group 335: `row.names = "EKLCYVALDFEQEMATAASSSSLEK"` and `col.names = #> "HQGVMVGMGQKDSYVGDEAQSK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -434,7 +439,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 20: `row.names = "GPRPPNQQQPIEGTDRVEPK"`, `col.names = +#> ℹ In group 20: `row.names = "GPRPPNQQQPIEGTDRVEPK"` and `col.names = #> "SQADKPVLAIQVLGTVK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -442,7 +447,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 6: `row.names = "ITYVANVNPGGWAPASVLR"`, `col.names = +#> ℹ In group 6: `row.names = "ITYVANVNPGGWAPASVLR"` and `col.names = #> "RHGSMVSLVSGASGYSATSTSSFK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -450,21 +455,21 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 3: `row.names = "GLSNLFLSCPIPK"`, `col.names = "LLLLAGVDR"`. +#> ℹ In group 3: `row.names = "GLSNLFLSCPIPK"` and `col.names = "LLLLAGVDR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. #> Warning: There were 18 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 37: `row.names = "ALSINTLVK"`, `col.names = "FASTVFPSDHIPSR"`. +#> ℹ In group 37: `row.names = "ALSINTLVK"` and `col.names = "FASTVFPSDHIPSR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 17 remaining warnings. #> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 8: `row.names = "ESTSYIEEHIDR"`, `col.names = +#> ℹ In group 8: `row.names = "ESTSYIEEHIDR"` and `col.names = #> "TQYLQSYGPEHLLTFSNLR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf diff --git a/reference/medpolish_estimate.html b/reference/medpolish_estimate.html index 92459aa35..80abf62d3 100644 --- a/reference/medpolish_estimate.html +++ b/reference/medpolish_estimate.html @@ -116,15 +116,15 @@

See also

aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), -medpolish_estimate_dfconfig(), medpolish_estimate_df(), +medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), -plot_hierarchies_line_df(), plot_hierarchies_line(), -rlm_estimate_dfconfig(), -rlm_estimate()

+plot_hierarchies_line_df(), +rlm_estimate(), +rlm_estimate_dfconfig()

diff --git a/reference/medpolish_estimate_df.html b/reference/medpolish_estimate_df.html index f0505f7b9..d1c05dc9a 100644 --- a/reference/medpolish_estimate_df.html +++ b/reference/medpolish_estimate_df.html @@ -125,31 +125,31 @@

See also

aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), -medpolish_estimate_dfconfig(), medpolish_estimate(), +medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), -plot_hierarchies_line_df(), plot_hierarchies_line(), -rlm_estimate_dfconfig(), -rlm_estimate()

+plot_hierarchies_line_df(), +rlm_estimate(), +rlm_estimate_dfconfig()

Other plotting: ContrastsPlotter, INTERNAL_FUNCTIONS_BY_FAMILY, UpSet_interaction_missing_stats(), UpSet_missing_stats(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), diff --git a/reference/medpolish_estimate_dfconfig.html b/reference/medpolish_estimate_dfconfig.html index 67e8aad0c..ca4aa06e4 100644 --- a/reference/medpolish_estimate_dfconfig.html +++ b/reference/medpolish_estimate_dfconfig.html @@ -111,15 +111,15 @@

See also

aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), -medpolish_estimate_df(), medpolish_estimate(), +medpolish_estimate_df(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), -plot_hierarchies_line_df(), plot_hierarchies_line(), -rlm_estimate_dfconfig(), -rlm_estimate()

+plot_hierarchies_line_df(), +rlm_estimate(), +rlm_estimate_dfconfig()

diff --git a/reference/medpolish_protein_estimates.html b/reference/medpolish_protein_estimates.html index 0bdce42fa..e4357b107 100644 --- a/reference/medpolish_protein_estimates.html +++ b/reference/medpolish_protein_estimates.html @@ -100,15 +100,15 @@

See also

aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), -medpolish_estimate_dfconfig(), -medpolish_estimate_df(), medpolish_estimate(), +medpolish_estimate_df(), +medpolish_estimate_dfconfig(), plot_estimate(), plot_hierarchies_add_quantline(), -plot_hierarchies_line_df(), plot_hierarchies_line(), -rlm_estimate_dfconfig(), -rlm_estimate()

+plot_hierarchies_line_df(), +rlm_estimate(), +rlm_estimate_dfconfig()

Other deprecated: INTERNAL_FUNCTIONS_BY_FAMILY, intensity_summary_by_hkeys(), diff --git a/reference/merge_contrasts_results.html b/reference/merge_contrasts_results.html index 470d1a993..9e4e00ba9 100644 --- a/reference/merge_contrasts_results.html +++ b/reference/merge_contrasts_results.html @@ -110,14 +110,13 @@

Arguments

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -134,12 +133,12 @@

See also

linfct_matrix_contrasts(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/missigness_histogram.html b/reference/missigness_histogram.html index 85958608e..0237fbe14 100644 --- a/reference/missigness_histogram.html +++ b/reference/missigness_histogram.html @@ -107,16 +107,16 @@

See also

UpSet_interaction_missing_stats(), UpSet_missing_stats(), medpolish_estimate_df(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), @@ -128,8 +128,8 @@

See also

aggregate_contrast(), get_contrast(), missigness_impute_factors_interactions(), -missingness_per_condition_cumsum(), -missingness_per_condition()

+missingness_per_condition(), +missingness_per_condition_cumsum()

diff --git a/reference/missigness_impute_factors_interactions.html b/reference/missigness_impute_factors_interactions.html index 05165d682..1fe0f8f9a 100644 --- a/reference/missigness_impute_factors_interactions.html +++ b/reference/missigness_impute_factors_interactions.html @@ -135,8 +135,8 @@

See also

aggregate_contrast(), get_contrast(), missigness_histogram(), -missingness_per_condition_cumsum(), -missingness_per_condition()

+missingness_per_condition(), +missingness_per_condition_cumsum()

diff --git a/reference/missingness_per_condition.html b/reference/missingness_per_condition.html index a65dd5972..4aafa06e1 100644 --- a/reference/missingness_per_condition.html +++ b/reference/missingness_per_condition.html @@ -109,12 +109,12 @@

See also

missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), diff --git a/reference/missingness_per_condition_cumsum.html b/reference/missingness_per_condition_cumsum.html index 18a46e897..57b2340d4 100644 --- a/reference/missingness_per_condition_cumsum.html +++ b/reference/missingness_per_condition_cumsum.html @@ -109,12 +109,12 @@

See also

missingness_per_condition(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), diff --git a/reference/model_analyse.html b/reference/model_analyse.html index 80dc6d602..d3f8d97cd 100644 --- a/reference/model_analyse.html +++ b/reference/model_analyse.html @@ -101,14 +101,13 @@

analyses lmer4 and lm models created using help function `strategy_lm` or `s

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -125,12 +124,12 @@

See also

linfct_matrix_contrasts(), merge_contrasts_results(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/model_summary.html b/reference/model_summary.html index 30a2c869b..6b27338db 100644 --- a/reference/model_summary.html +++ b/reference/model_summary.html @@ -102,14 +102,13 @@

Arguments

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -126,12 +125,12 @@

See also

linfct_matrix_contrasts(), merge_contrasts_results(), model_analyse(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/moderated_p_limma.html b/reference/moderated_p_limma.html index 1ce2e1bec..50d9bb1ba 100644 --- a/reference/moderated_p_limma.html +++ b/reference/moderated_p_limma.html @@ -102,14 +102,13 @@

Moderate p-values - limma approach

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -129,9 +128,9 @@

See also

model_summary(), moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/moderated_p_limma_long.html b/reference/moderated_p_limma_long.html index f215dba47..85ed344c2 100644 --- a/reference/moderated_p_limma_long.html +++ b/reference/moderated_p_limma_long.html @@ -111,14 +111,13 @@

Arguments

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -138,9 +137,9 @@

See also

model_summary(), moderated_p_limma(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/my_contest.html b/reference/my_contest.html index 489254d27..7aa318593 100644 --- a/reference/my_contest.html +++ b/reference/my_contest.html @@ -110,14 +110,13 @@

Arguments

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -135,11 +134,11 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/my_contrast.html b/reference/my_contrast.html index ef6b61cab..4e002c2cf 100644 --- a/reference/my_contrast.html +++ b/reference/my_contrast.html @@ -124,14 +124,13 @@

Arguments

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -149,8 +148,8 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), my_contrast_V1(), my_contrast_V2(), diff --git a/reference/my_contrast_V1.html b/reference/my_contrast_V1.html index 84052c5ef..01f12f5c8 100644 --- a/reference/my_contrast_V1.html +++ b/reference/my_contrast_V1.html @@ -110,14 +110,13 @@

Arguments

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -135,11 +134,11 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), -my_contrast_V2(), my_contrast(), +my_contrast_V2(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/my_contrast_V2.html b/reference/my_contrast_V2.html index 0f7ac2f29..13f620704 100644 --- a/reference/my_contrast_V2.html +++ b/reference/my_contrast_V2.html @@ -110,14 +110,13 @@

Arguments

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -135,11 +134,11 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), -my_contrast_V1(), my_contrast(), +my_contrast_V1(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/my_glht.html b/reference/my_glht.html index b509fecbe..1742e3bf6 100644 --- a/reference/my_glht.html +++ b/reference/my_glht.html @@ -96,14 +96,13 @@

apply multcomp::glht method to linfct

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -121,12 +120,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), plot_lmer_peptide_noRandom(), diff --git a/reference/normalize_log2_robscale.html b/reference/normalize_log2_robscale.html index a515a7802..9b669066e 100644 --- a/reference/normalize_log2_robscale.html +++ b/reference/normalize_log2_robscale.html @@ -117,8 +117,8 @@

See also

filter_proteins_by_peptide_count(), get_robscales(), robust_scale(), -scale_with_subset_by_factors(), -scale_with_subset()

+scale_with_subset(), +scale_with_subset_by_factors()

diff --git a/reference/nr_B_in_A_per_sample.html b/reference/nr_B_in_A_per_sample.html index 871aba9c2..b2de581c9 100644 --- a/reference/nr_B_in_A_per_sample.html +++ b/reference/nr_B_in_A_per_sample.html @@ -97,8 +97,8 @@

how many peptides per protein in each sample

See also

Other summary: INTERNAL_FUNCTIONS_BY_FAMILY, -hierarchy_counts_sample(), hierarchy_counts(), +hierarchy_counts_sample(), summarize_hierarchy()

diff --git a/reference/pivot_model_contrasts_2_Wide.html b/reference/pivot_model_contrasts_2_Wide.html index ddc1f3a2f..90c246079 100644 --- a/reference/pivot_model_contrasts_2_Wide.html +++ b/reference/pivot_model_contrasts_2_Wide.html @@ -101,14 +101,13 @@

pivot model contrasts matrix to wide format produced by `contrasts_linfct` a

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -126,12 +125,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), plot_lmer_model_and_data(), plot_lmer_peptide_noRandom(), diff --git a/reference/plot_NA_heatmap.html b/reference/plot_NA_heatmap.html index 2dd400c89..1a9ae0425 100644 --- a/reference/plot_NA_heatmap.html +++ b/reference/plot_NA_heatmap.html @@ -102,15 +102,15 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), diff --git a/reference/plot_estimate.html b/reference/plot_estimate.html index dd2df57c3..d0ae5a4c6 100644 --- a/reference/plot_estimate.html +++ b/reference/plot_estimate.html @@ -120,15 +120,15 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), @@ -139,15 +139,15 @@

See also

aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), -medpolish_estimate_dfconfig(), -medpolish_estimate_df(), medpolish_estimate(), +medpolish_estimate_df(), +medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_hierarchies_add_quantline(), -plot_hierarchies_line_df(), plot_hierarchies_line(), -rlm_estimate_dfconfig(), -rlm_estimate()

+plot_hierarchies_line_df(), +rlm_estimate(), +rlm_estimate_dfconfig()

diff --git a/reference/plot_heatmap.html b/reference/plot_heatmap.html index fda94e225..7bb7b02b9 100644 --- a/reference/plot_heatmap.html +++ b/reference/plot_heatmap.html @@ -112,15 +112,15 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), diff --git a/reference/plot_heatmap_cor.html b/reference/plot_heatmap_cor.html index b67193866..8bca66072 100644 --- a/reference/plot_heatmap_cor.html +++ b/reference/plot_heatmap_cor.html @@ -108,15 +108,15 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), plot_heatmap(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), diff --git a/reference/plot_hierarchies_add_quantline.html b/reference/plot_hierarchies_add_quantline.html index be63f97be..43d889728 100644 --- a/reference/plot_hierarchies_add_quantline.html +++ b/reference/plot_hierarchies_add_quantline.html @@ -100,15 +100,15 @@

See also

aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), -medpolish_estimate_dfconfig(), -medpolish_estimate_df(), medpolish_estimate(), +medpolish_estimate_df(), +medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), -plot_hierarchies_line_df(), plot_hierarchies_line(), -rlm_estimate_dfconfig(), -rlm_estimate()

+plot_hierarchies_line_df(), +rlm_estimate(), +rlm_estimate_dfconfig()

Other plotting: ContrastsPlotter, INTERNAL_FUNCTIONS_BY_FAMILY, @@ -116,15 +116,15 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), diff --git a/reference/plot_hierarchies_boxplot-1.png b/reference/plot_hierarchies_boxplot-1.png index dfa07c60a..368faff1e 100644 Binary files a/reference/plot_hierarchies_boxplot-1.png and b/reference/plot_hierarchies_boxplot-1.png differ diff --git a/reference/plot_hierarchies_boxplot.html b/reference/plot_hierarchies_boxplot.html index b01bd3e53..6c0cd897c 100644 --- a/reference/plot_hierarchies_boxplot.html +++ b/reference/plot_hierarchies_boxplot.html @@ -136,8 +136,10 @@

Examples

#> Column added : log2_Area res <- plot_hierarchies_boxplot_df(data, config) res$boxplot[[1]] -#> Warning: Removed 143 rows containing non-finite values (`stat_boxplot()`). -#> Warning: Removed 143 rows containing missing values (`position_quasirandom()`). +#> Warning: Removed 143 rows containing non-finite outside the scale range +#> (`stat_boxplot()`). +#> Warning: Removed 143 rows containing missing values or values outside the scale range +#> (`position_quasirandom()`). hierarchy = config$table$hierarchy_keys_depth() diff --git a/reference/plot_hierarchies_boxplot_df-1.png b/reference/plot_hierarchies_boxplot_df-1.png index 6fb39eea1..51724e02f 100644 Binary files a/reference/plot_hierarchies_boxplot_df-1.png and b/reference/plot_hierarchies_boxplot_df-1.png differ diff --git a/reference/plot_hierarchies_boxplot_df-2.png b/reference/plot_hierarchies_boxplot_df-2.png index 6fb39eea1..51724e02f 100644 Binary files a/reference/plot_hierarchies_boxplot_df-2.png and b/reference/plot_hierarchies_boxplot_df-2.png differ diff --git a/reference/plot_hierarchies_boxplot_df-3.png b/reference/plot_hierarchies_boxplot_df-3.png index 088b741f0..df20bac1f 100644 Binary files a/reference/plot_hierarchies_boxplot_df-3.png and b/reference/plot_hierarchies_boxplot_df-3.png differ diff --git a/reference/plot_hierarchies_boxplot_df-4.png b/reference/plot_hierarchies_boxplot_df-4.png index c4114ac89..ddc186f2d 100644 Binary files a/reference/plot_hierarchies_boxplot_df-4.png and b/reference/plot_hierarchies_boxplot_df-4.png differ diff --git a/reference/plot_hierarchies_boxplot_df-5.png b/reference/plot_hierarchies_boxplot_df-5.png index 91d885694..9014f2a0f 100644 Binary files a/reference/plot_hierarchies_boxplot_df-5.png and b/reference/plot_hierarchies_boxplot_df-5.png differ diff --git a/reference/plot_hierarchies_boxplot_df.html b/reference/plot_hierarchies_boxplot_df.html index 49621afab..f88016303 100644 --- a/reference/plot_hierarchies_boxplot_df.html +++ b/reference/plot_hierarchies_boxplot_df.html @@ -125,15 +125,15 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), @@ -155,20 +155,26 @@

Examples

res <- plot_hierarchies_boxplot_df(analysis,config) res$boxplot[[1]] -#> Warning: Removed 8 rows containing non-finite values (`stat_boxplot()`). -#> Warning: Removed 8 rows containing missing values (`position_quasirandom()`). +#> Warning: Removed 8 rows containing non-finite outside the scale range +#> (`stat_boxplot()`). +#> Warning: Removed 8 rows containing missing values or values outside the scale range +#> (`position_quasirandom()`). res <- plot_hierarchies_boxplot_df(analysis,config,config$table$hierarchy_keys()[1]) res$boxplot[[1]] -#> Warning: Removed 8 rows containing non-finite values (`stat_boxplot()`). -#> Warning: Removed 8 rows containing missing values (`position_quasirandom()`). +#> Warning: Removed 8 rows containing non-finite outside the scale range +#> (`stat_boxplot()`). +#> Warning: Removed 8 rows containing missing values or values outside the scale range +#> (`position_quasirandom()`). res <- plot_hierarchies_boxplot_df(analysis,config, config$table$hierarchy_keys()[1], facet_grid_on = config$table$hierarchy_keys()[2]) res$boxplot[[1]] -#> Warning: Removed 8 rows containing non-finite values (`stat_boxplot()`). -#> Warning: Removed 8 rows containing missing values (`position_quasirandom()`). +#> Warning: Removed 8 rows containing non-finite outside the scale range +#> (`stat_boxplot()`). +#> Warning: Removed 8 rows containing missing values or values outside the scale range +#> (`position_quasirandom()`). res$boxplot[[2]] @@ -183,8 +189,9 @@

Examples

res <- plot_hierarchies_boxplot_df(iostar$data,iostar$config) res$boxplot[[1]] -#> Warning: Removed 1 rows containing non-finite values (`stat_boxplot()`). -#> Warning: Removed 1 rows containing missing values (`position_quasirandom()`). +#> Warning: Removed 1 row containing non-finite outside the scale range (`stat_boxplot()`). +#> Warning: Removed 1 row containing missing values or values outside the scale range +#> (`position_quasirandom()`). res <- plot_hierarchies_boxplot_df(iostar$data,iostar$config, iostar$config$table$hierarchy_keys()[1]) diff --git a/reference/plot_hierarchies_line-3.png b/reference/plot_hierarchies_line-3.png index 3740ca8b6..cb182d973 100644 Binary files a/reference/plot_hierarchies_line-3.png and b/reference/plot_hierarchies_line-3.png differ diff --git a/reference/plot_hierarchies_line.html b/reference/plot_hierarchies_line.html index bc7e3a536..8578226a8 100644 --- a/reference/plot_hierarchies_line.html +++ b/reference/plot_hierarchies_line.html @@ -124,15 +124,15 @@

See also

aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), -medpolish_estimate_dfconfig(), -medpolish_estimate_df(), medpolish_estimate(), +medpolish_estimate_df(), +medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), plot_hierarchies_line_df(), -rlm_estimate_dfconfig(), -rlm_estimate()

+rlm_estimate(), +rlm_estimate_dfconfig()

Other plotting: ContrastsPlotter, INTERNAL_FUNCTIONS_BY_FAMILY, @@ -140,12 +140,12 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), plot_hierarchies_line_df(), @@ -170,8 +170,10 @@

Examples

dplyr::group_by_at(config$table$hierarchy_keys_depth()) |> tidyr::nest() prolfqua::plot_hierarchies_line(xnested$data[[1]], xnested$protein_Id[[1]],config ) -#> Warning: Removed 7 rows containing missing values (`geom_point()`). -#> Warning: Removed 1 row containing missing values (`geom_line()`). +#> Warning: Removed 7 rows containing missing values or values outside the scale range +#> (`geom_point()`). +#> Warning: Removed 1 row containing missing values or values outside the scale range +#> (`geom_line()`). bb <- prolfqua_data('data_skylineSRM_HL_A') @@ -185,16 +187,20 @@

Examples

"DUM", conf, separate = TRUE) -#> Warning: Removed 802 rows containing missing values (`geom_point()`). -#> Warning: Removed 462 rows containing missing values (`geom_line()`). +#> Warning: Removed 802 rows containing missing values or values outside the scale range +#> (`geom_point()`). +#> Warning: Removed 462 rows containing missing values or values outside the scale range +#> (`geom_line()`). prolfqua::plot_hierarchies_line(nest$data[[1]], "DUM", conf, separate = TRUE, show.legend = TRUE) -#> Warning: Removed 802 rows containing missing values (`geom_point()`). -#> Warning: Removed 462 rows containing missing values (`geom_line()`). +#> Warning: Removed 802 rows containing missing values or values outside the scale range +#> (`geom_point()`). +#> Warning: Removed 462 rows containing missing values or values outside the scale range +#> (`geom_line()`).
diff --git a/reference/plot_hierarchies_line_df-3.png b/reference/plot_hierarchies_line_df-3.png index 43058e44e..c501cf25f 100644 Binary files a/reference/plot_hierarchies_line_df-3.png and b/reference/plot_hierarchies_line_df-3.png differ diff --git a/reference/plot_hierarchies_line_df.html b/reference/plot_hierarchies_line_df.html index f03e2cfb9..89d5abb42 100644 --- a/reference/plot_hierarchies_line_df.html +++ b/reference/plot_hierarchies_line_df.html @@ -111,15 +111,15 @@

See also

aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), -medpolish_estimate_dfconfig(), -medpolish_estimate_df(), medpolish_estimate(), +medpolish_estimate_df(), +medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), plot_hierarchies_line(), -rlm_estimate_dfconfig(), -rlm_estimate()

+rlm_estimate(), +rlm_estimate_dfconfig()

Other plotting: ContrastsPlotter, INTERNAL_FUNCTIONS_BY_FAMILY, @@ -127,12 +127,12 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), plot_hierarchies_line(), @@ -157,18 +157,22 @@

Examples

res <- plot_hierarchies_line_df(istar_data, config) res[[1]] #> Warning: NaNs produced -#> Warning: Transformation introduced infinite values in continuous y-axis +#> Warning: log-10 transformation introduced infinite values. #> Warning: NaNs produced -#> Warning: Transformation introduced infinite values in continuous y-axis -#> Warning: Removed 121 rows containing missing values (`geom_point()`). -#> Warning: Removed 88 rows containing missing values (`geom_line()`). +#> Warning: log-10 transformation introduced infinite values. +#> Warning: Removed 121 rows containing missing values or values outside the scale range +#> (`geom_point()`). +#> Warning: Removed 88 rows containing missing values or values outside the scale range +#> (`geom_line()`). config$table$is_response_transformed <- TRUE res <- plot_hierarchies_line_df(istar_data, config) res[[1]] -#> Warning: Removed 37 rows containing missing values (`geom_point()`). -#> Warning: Removed 4 rows containing missing values (`geom_line()`). +#> Warning: Removed 37 rows containing missing values or values outside the scale range +#> (`geom_point()`). +#> Warning: Removed 4 rows containing missing values or values outside the scale range +#> (`geom_line()`). istar <- prolfqua_data('data_ionstar')$filtered() @@ -179,16 +183,20 @@

Examples

config$table$is_response_transformed #> [1] FALSE res[[1]] -#> Warning: Removed 16 rows containing missing values (`geom_point()`). -#> Warning: Removed 2 rows containing missing values (`geom_line()`). +#> Warning: Removed 16 rows containing missing values or values outside the scale range +#> (`geom_point()`). +#> Warning: Removed 2 rows containing missing values or values outside the scale range +#> (`geom_line()`). config$table$is_response_transformed <- TRUE res <- plot_hierarchies_line_df(istar_data, config) config$table$is_response_transformed #> [1] TRUE res[[1]] -#> Warning: Removed 16 rows containing missing values (`geom_point()`). -#> Warning: Removed 2 rows containing missing values (`geom_line()`). +#> Warning: Removed 16 rows containing missing values or values outside the scale range +#> (`geom_point()`). +#> Warning: Removed 2 rows containing missing values or values outside the scale range +#> (`geom_line()`). #TODO make it work for other hiearachy levels. diff --git a/reference/plot_intensity_distribution_violin-1.png b/reference/plot_intensity_distribution_violin-1.png index 5967ab275..9c5c55cb3 100644 Binary files a/reference/plot_intensity_distribution_violin-1.png and b/reference/plot_intensity_distribution_violin-1.png differ diff --git a/reference/plot_intensity_distribution_violin-2.png b/reference/plot_intensity_distribution_violin-2.png index 1cb08ccdb..dc3b6a84b 100644 Binary files a/reference/plot_intensity_distribution_violin-2.png and b/reference/plot_intensity_distribution_violin-2.png differ diff --git a/reference/plot_intensity_distribution_violin-3.png b/reference/plot_intensity_distribution_violin-3.png index 89c8cef9e..cbbbe08c7 100644 Binary files a/reference/plot_intensity_distribution_violin-3.png and b/reference/plot_intensity_distribution_violin-3.png differ diff --git a/reference/plot_intensity_distribution_violin-4.png b/reference/plot_intensity_distribution_violin-4.png index da3a9ee91..addcc0f8c 100644 Binary files a/reference/plot_intensity_distribution_violin-4.png and b/reference/plot_intensity_distribution_violin-4.png differ diff --git a/reference/plot_intensity_distribution_violin.html b/reference/plot_intensity_distribution_violin.html index 54eb413fb..be8fb39a1 100644 --- a/reference/plot_intensity_distribution_violin.html +++ b/reference/plot_intensity_distribution_violin.html @@ -120,16 +120,16 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_pca(), plot_raster(), plot_sample_correlation(), @@ -141,16 +141,16 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_pca(), plot_raster(), plot_sample_correlation(), @@ -168,14 +168,18 @@

Examples

analysis <- istar$data plot_intensity_distribution_violin(analysis, config) -#> Warning: Removed 36 rows containing non-finite values (`stat_ydensity()`). -#> Warning: Removed 36 rows containing non-finite values (`stat_summary()`). +#> Warning: Removed 36 rows containing non-finite outside the scale range +#> (`stat_ydensity()`). +#> Warning: Removed 36 rows containing non-finite outside the scale range +#> (`stat_summary()`). analysis <- transform_work_intensity(analysis, config, log2) #> Column added : log2_abundance plot_intensity_distribution_violin(analysis, config) -#> Warning: Removed 36 rows containing non-finite values (`stat_ydensity()`). -#> Warning: Removed 36 rows containing non-finite values (`stat_summary()`). +#> Warning: Removed 36 rows containing non-finite outside the scale range +#> (`stat_ydensity()`). +#> Warning: Removed 36 rows containing non-finite outside the scale range +#> (`stat_summary()`). @@ -186,12 +190,14 @@

Examples

config <- istar$config analysis <- istar$data plot_intensity_distribution_density(analysis, config) -#> Warning: Removed 36 rows containing non-finite values (`stat_density()`). +#> Warning: Removed 36 rows containing non-finite outside the scale range +#> (`stat_density()`). analysis <- transform_work_intensity(analysis, config, log2) #> Column added : log2_abundance plot_intensity_distribution_density(analysis, config) -#> Warning: Removed 36 rows containing non-finite values (`stat_density()`). +#> Warning: Removed 36 rows containing non-finite outside the scale range +#> (`stat_density()`).
diff --git a/reference/plot_lmer_model_and_data-1.png b/reference/plot_lmer_model_and_data-1.png index 2cfcaa460..31b42c48f 100644 Binary files a/reference/plot_lmer_model_and_data-1.png and b/reference/plot_lmer_model_and_data-1.png differ diff --git a/reference/plot_lmer_model_and_data.html b/reference/plot_lmer_model_and_data.html index 460dc47b5..cfba40953 100644 --- a/reference/plot_lmer_model_and_data.html +++ b/reference/plot_lmer_model_and_data.html @@ -96,14 +96,13 @@

Make model plot with title - protein Name.

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -121,12 +120,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_peptide_noRandom(), diff --git a/reference/plot_lmer_peptide_noRandom-1.png b/reference/plot_lmer_peptide_noRandom-1.png index 8c3f08707..9923bc13c 100644 Binary files a/reference/plot_lmer_peptide_noRandom-1.png and b/reference/plot_lmer_peptide_noRandom-1.png differ diff --git a/reference/plot_lmer_peptide_noRandom-2.png b/reference/plot_lmer_peptide_noRandom-2.png index 7f92616d2..32725a6b8 100644 Binary files a/reference/plot_lmer_peptide_noRandom-2.png and b/reference/plot_lmer_peptide_noRandom-2.png differ diff --git a/reference/plot_lmer_peptide_noRandom.html b/reference/plot_lmer_peptide_noRandom.html index 3f07a8561..2259281eb 100644 --- a/reference/plot_lmer_peptide_noRandom.html +++ b/reference/plot_lmer_peptide_noRandom.html @@ -106,14 +106,13 @@

Arguments

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -131,12 +130,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/plot_lmer_peptide_predictions.html b/reference/plot_lmer_peptide_predictions.html index 6ffbbfdfc..7ac165853 100644 --- a/reference/plot_lmer_peptide_predictions.html +++ b/reference/plot_lmer_peptide_predictions.html @@ -96,14 +96,13 @@

Plot prdictions

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -121,12 +120,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/plot_lmer_predicted_interactions-1.png b/reference/plot_lmer_predicted_interactions-1.png index 1f5e85f60..55ca768e6 100644 Binary files a/reference/plot_lmer_predicted_interactions-1.png and b/reference/plot_lmer_predicted_interactions-1.png differ diff --git a/reference/plot_lmer_predicted_interactions.html b/reference/plot_lmer_predicted_interactions.html index 2fc3cd842..8055c8e4d 100644 --- a/reference/plot_lmer_predicted_interactions.html +++ b/reference/plot_lmer_predicted_interactions.html @@ -96,14 +96,13 @@

Add predicted values for each interaction

See also

Other modelling: +Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, -ContrastsSAINTexpress, ContrastsTable, -Contrasts, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, @@ -121,12 +120,12 @@

See also

merge_contrasts_results(), model_analyse(), model_summary(), -moderated_p_limma_long(), moderated_p_limma(), +moderated_p_limma_long(), my_contest(), +my_contrast(), my_contrast_V1(), my_contrast_V2(), -my_contrast(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), diff --git a/reference/plot_pca-1.png b/reference/plot_pca-1.png index a12c5a6d0..2825f9333 100644 Binary files a/reference/plot_pca-1.png and b/reference/plot_pca-1.png differ diff --git a/reference/plot_pca.html b/reference/plot_pca.html index 76c6585f5..6eac99657 100644 --- a/reference/plot_pca.html +++ b/reference/plot_pca.html @@ -102,16 +102,16 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_raster(), plot_sample_correlation(), diff --git a/reference/plot_raster.html b/reference/plot_raster.html index 192145aad..abc7f716f 100644 --- a/reference/plot_raster.html +++ b/reference/plot_raster.html @@ -131,16 +131,16 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_sample_correlation(), diff --git a/reference/plot_sample_correlation.html b/reference/plot_sample_correlation.html index c3939227a..6bc4655c2 100644 --- a/reference/plot_sample_correlation.html +++ b/reference/plot_sample_correlation.html @@ -112,16 +112,16 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), diff --git a/reference/plot_screeplot-1.png b/reference/plot_screeplot-1.png index 59324dcac..173ba806e 100644 Binary files a/reference/plot_screeplot-1.png and b/reference/plot_screeplot-1.png differ diff --git a/reference/plot_screeplot-2.png b/reference/plot_screeplot-2.png index 689662996..59db3e687 100644 Binary files a/reference/plot_screeplot-2.png and b/reference/plot_screeplot-2.png differ diff --git a/reference/plot_screeplot-3.png b/reference/plot_screeplot-3.png index a770c9ace..abec2acb2 100644 Binary files a/reference/plot_screeplot-3.png and b/reference/plot_screeplot-3.png differ diff --git a/reference/plot_screeplot.html b/reference/plot_screeplot.html index a95b6fe5d..07e1a35bc 100644 --- a/reference/plot_screeplot.html +++ b/reference/plot_screeplot.html @@ -102,16 +102,16 @@

See also

UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), -missingness_per_condition_cumsum(), missingness_per_condition(), +missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), -plot_heatmap_cor(), plot_heatmap(), +plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), diff --git a/reference/plot_stat_density-1.png b/reference/plot_stat_density-1.png index c913c58da..27ffd451e 100644 Binary files a/reference/plot_stat_density-1.png and b/reference/plot_stat_density-1.png differ diff --git a/reference/plot_stat_density-2.png b/reference/plot_stat_density-2.png index a0b529c90..cb6feedb0 100644 Binary files a/reference/plot_stat_density-2.png and b/reference/plot_stat_density-2.png differ diff --git a/reference/plot_stat_density-3.png b/reference/plot_stat_density-3.png index cbf55d361..f45f1d3e0 100644 Binary files a/reference/plot_stat_density-3.png and b/reference/plot_stat_density-3.png differ diff --git a/reference/plot_stat_density.html b/reference/plot_stat_density.html index 91dc9d678..79c02f64e 100644 --- a/reference/plot_stat_density.html +++ b/reference/plot_stat_density.html @@ -121,11 +121,11 @@

See also

Other stats: INTERNAL_FUNCTIONS_BY_FAMILY, lfq_power_t_test_proteins(), -lfq_power_t_test_quantiles_V2(), lfq_power_t_test_quantiles(), +lfq_power_t_test_quantiles_V2(), plot_stat_density_median(), -plot_stat_violin_median(), plot_stat_violin(), +plot_stat_violin_median(), plot_stdv_vs_mean(), pooled_V2(), summarize_stats()

@@ -142,13 +142,16 @@

Examples

res <- summarize_stats(data, config) #> completing cases plot_stat_density(res, config, stat = "mean") -#> Warning: Removed 368 rows containing non-finite values (`stat_density()`). +#> Warning: Removed 368 rows containing non-finite outside the scale range +#> (`stat_density()`). plot_stat_density(res, config, stat = "sd") -#> Warning: Removed 846 rows containing non-finite values (`stat_density()`). +#> Warning: Removed 846 rows containing non-finite outside the scale range +#> (`stat_density()`). plot_stat_density(res, config, stat = "CV") -#> Warning: Removed 846 rows containing non-finite values (`stat_density()`). +#> Warning: Removed 846 rows containing non-finite outside the scale range +#> (`stat_density()`).
diff --git a/reference/plot_stat_density_median-1.png b/reference/plot_stat_density_median-1.png index e1edb7ae0..33bf04ae7 100644 Binary files a/reference/plot_stat_density_median-1.png and b/reference/plot_stat_density_median-1.png differ diff --git a/reference/plot_stat_density_median-2.png b/reference/plot_stat_density_median-2.png index ef28bc0bd..d50ce91d6 100644 Binary files a/reference/plot_stat_density_median-2.png and b/reference/plot_stat_density_median-2.png differ diff --git a/reference/plot_stat_density_median-3.png b/reference/plot_stat_density_median-3.png index a9bf44ebb..af730b57b 100644 Binary files a/reference/plot_stat_density_median-3.png and b/reference/plot_stat_density_median-3.png differ diff --git a/reference/plot_stat_density_median.html b/reference/plot_stat_density_median.html index d2e25bf8a..661f30c29 100644 --- a/reference/plot_stat_density_median.html +++ b/reference/plot_stat_density_median.html @@ -121,11 +121,11 @@

See also

Other stats: INTERNAL_FUNCTIONS_BY_FAMILY, lfq_power_t_test_proteins(), -lfq_power_t_test_quantiles_V2(), lfq_power_t_test_quantiles(), +lfq_power_t_test_quantiles_V2(), plot_stat_density(), -plot_stat_violin_median(), plot_stat_violin(), +plot_stat_violin_median(), plot_stdv_vs_mean(), pooled_V2(), summarize_stats()

diff --git a/reference/plot_stat_violin-1.png b/reference/plot_stat_violin-1.png index 1a7dceed0..c2ae6b888 100644 Binary files a/reference/plot_stat_violin-1.png and b/reference/plot_stat_violin-1.png differ diff --git a/reference/plot_stat_violin-2.png b/reference/plot_stat_violin-2.png index 34e7509e0..c56293413 100644 Binary files a/reference/plot_stat_violin-2.png and b/reference/plot_stat_violin-2.png differ diff --git a/reference/plot_stat_violin-3.png b/reference/plot_stat_violin-3.png index 14541c994..cc3f638cc 100644 Binary files a/reference/plot_stat_violin-3.png and b/reference/plot_stat_violin-3.png differ diff --git a/reference/plot_stat_violin.html b/reference/plot_stat_violin.html index 5400d24cb..5ed2242de 100644 --- a/reference/plot_stat_violin.html +++ b/reference/plot_stat_violin.html @@ -112,10 +112,10 @@

See also

Other stats: INTERNAL_FUNCTIONS_BY_FAMILY, lfq_power_t_test_proteins(), -lfq_power_t_test_quantiles_V2(), lfq_power_t_test_quantiles(), -plot_stat_density_median(), +lfq_power_t_test_quantiles_V2(), plot_stat_density(), +plot_stat_density_median(), plot_stat_violin_median(), plot_stdv_vs_mean(), pooled_V2(), @@ -135,16 +135,22 @@

Examples

res <- summarize_stats(data, config) #> completing cases plot_stat_violin(res, config, stat = "mean") -#> Warning: Removed 368 rows containing non-finite values (`stat_ydensity()`). -#> Warning: Removed 368 rows containing non-finite values (`stat_summary()`). +#> Warning: Removed 368 rows containing non-finite outside the scale range +#> (`stat_ydensity()`). +#> Warning: Removed 368 rows containing non-finite outside the scale range +#> (`stat_summary()`). plot_stat_violin(res, config, stat = "sd") -#> Warning: Removed 846 rows containing non-finite values (`stat_ydensity()`). -#> Warning: Removed 846 rows containing non-finite values (`stat_summary()`). +#> Warning: Removed 846 rows containing non-finite outside the scale range +#> (`stat_ydensity()`). +#> Warning: Removed 846 rows containing non-finite outside the scale range +#> (`stat_summary()`). plot_stat_violin(res, config, stat = "CV") -#> Warning: Removed 846 rows containing non-finite values (`stat_ydensity()`). -#> Warning: Removed 846 rows containing non-finite values (`stat_summary()`). +#> Warning: Removed 846 rows containing non-finite outside the scale range +#> (`stat_ydensity()`). +#> Warning: Removed 846 rows containing non-finite outside the scale range +#> (`stat_summary()`).
diff --git a/reference/plot_stat_violin_median.html b/reference/plot_stat_violin_median.html index 86680363d..6e9bc92c5 100644 --- a/reference/plot_stat_violin_median.html +++ b/reference/plot_stat_violin_median.html @@ -112,10 +112,10 @@

See also

Other stats: INTERNAL_FUNCTIONS_BY_FAMILY, lfq_power_t_test_proteins(), -lfq_power_t_test_quantiles_V2(), lfq_power_t_test_quantiles(), -plot_stat_density_median(), +lfq_power_t_test_quantiles_V2(), plot_stat_density(), +plot_stat_density_median(), plot_stat_violin(), plot_stdv_vs_mean(), pooled_V2(), diff --git a/reference/plot_stdv_vs_mean.html b/reference/plot_stdv_vs_mean.html index 019b5980e..f972bb7d1 100644 --- a/reference/plot_stdv_vs_mean.html +++ b/reference/plot_stdv_vs_mean.html @@ -112,12 +112,12 @@

See also

Other stats: INTERNAL_FUNCTIONS_BY_FAMILY, lfq_power_t_test_proteins(), -lfq_power_t_test_quantiles_V2(), lfq_power_t_test_quantiles(), -plot_stat_density_median(), +lfq_power_t_test_quantiles_V2(), plot_stat_density(), -plot_stat_violin_median(), +plot_stat_density_median(), plot_stat_violin(), +plot_stat_violin_median(), pooled_V2(), summarize_stats()

@@ -136,8 +136,10 @@

Examples

plot_stdv_vs_mean(res, config) #> `geom_smooth()` using formula = 'y ~ x' -#> Warning: Removed 846 rows containing non-finite values (`stat_smooth()`). -#> Warning: Removed 846 rows containing missing values (`geom_point()`). +#> Warning: Removed 846 rows containing non-finite outside the scale range +#> (`stat_smooth()`). +#> Warning: Removed 846 rows containing missing values or values outside the scale range +#> (`geom_point()`). datalog2 <- transform_work_intensity(data, config, log2) #> Column added : log2_peptide.intensity @@ -145,8 +147,10 @@

Examples

#> completing cases plot_stdv_vs_mean(statlog2, config) #> `geom_smooth()` using formula = 'y ~ x' -#> Warning: Removed 846 rows containing non-finite values (`stat_smooth()`). -#> Warning: Removed 846 rows containing missing values (`geom_point()`). +#> Warning: Removed 846 rows containing non-finite outside the scale range +#> (`stat_smooth()`). +#> Warning: Removed 846 rows containing missing values or values outside the scale range +#> (`geom_point()`). config$table$get_response() #> [1] "log2_peptide.intensity" @@ -158,8 +162,10 @@

Examples

#> completing cases plot_stdv_vs_mean(ressqrt, config) #> `geom_smooth()` using formula = 'y ~ x' -#> Warning: Removed 846 rows containing non-finite values (`stat_smooth()`). -#> Warning: Removed 846 rows containing missing values (`geom_point()`). +#> Warning: Removed 846 rows containing non-finite outside the scale range +#> (`stat_smooth()`). +#> Warning: Removed 846 rows containing missing values or values outside the scale range +#> (`geom_point()`).
diff --git a/reference/pooled_var.html b/reference/pooled_var.html index beef42766..f97230e1f 100644 --- a/reference/pooled_var.html +++ b/reference/pooled_var.html @@ -118,23 +118,23 @@

See also

Other stats: INTERNAL_FUNCTIONS_BY_FAMILY, lfq_power_t_test_proteins(), -lfq_power_t_test_quantiles_V2(), lfq_power_t_test_quantiles(), -plot_stat_density_median(), +lfq_power_t_test_quantiles_V2(), plot_stat_density(), -plot_stat_violin_median(), +plot_stat_density_median(), plot_stat_violin(), +plot_stat_violin_median(), plot_stdv_vs_mean(), summarize_stats()

Other stats: INTERNAL_FUNCTIONS_BY_FAMILY, lfq_power_t_test_proteins(), -lfq_power_t_test_quantiles_V2(), lfq_power_t_test_quantiles(), -plot_stat_density_median(), +lfq_power_t_test_quantiles_V2(), plot_stat_density(), -plot_stat_violin_median(), +plot_stat_density_median(), plot_stat_violin(), +plot_stat_violin_median(), plot_stdv_vs_mean(), summarize_stats()

diff --git a/reference/prolfqua_data.html b/reference/prolfqua_data.html index 3a72cfea1..7d991dc84 100644 --- a/reference/prolfqua_data.html +++ b/reference/prolfqua_data.html @@ -113,8 +113,8 @@

See also

data_basicModel_p1807, data_benchmarkExample, data_checksummarizationrobust87, -data_checksummarizerobust69, data_checksummarizerobust, +data_checksummarizerobust69, data_correlatedPeptideList, data_factor_levelContrasts, data_interactionModel_p1807, diff --git a/reference/rlm_estimate.html b/reference/rlm_estimate.html index 170b9bbb5..9d9df462f 100644 --- a/reference/rlm_estimate.html +++ b/reference/rlm_estimate.html @@ -118,14 +118,14 @@

See also

aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), -medpolish_estimate_dfconfig(), -medpolish_estimate_df(), medpolish_estimate(), +medpolish_estimate_df(), +medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), rlm_estimate_dfconfig()

diff --git a/reference/rlm_estimate_dfconfig.html b/reference/rlm_estimate_dfconfig.html index fb57c6805..6e57d9b57 100644 --- a/reference/rlm_estimate_dfconfig.html +++ b/reference/rlm_estimate_dfconfig.html @@ -111,14 +111,14 @@

See also

aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), -medpolish_estimate_dfconfig(), -medpolish_estimate_df(), medpolish_estimate(), +medpolish_estimate_df(), +medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), -plot_hierarchies_line_df(), plot_hierarchies_line(), +plot_hierarchies_line_df(), rlm_estimate()

diff --git a/reference/robust_scale.html b/reference/robust_scale.html index 9312e7cd1..3d6094600 100644 --- a/reference/robust_scale.html +++ b/reference/robust_scale.html @@ -101,8 +101,8 @@

See also

filter_proteins_by_peptide_count(), get_robscales(), normalize_log2_robscale(), -scale_with_subset_by_factors(), -scale_with_subset()

+scale_with_subset(), +scale_with_subset_by_factors()

diff --git a/reference/saintExpress.html b/reference/saintExpress.html deleted file mode 100644 index d34b42dee..000000000 --- a/reference/saintExpress.html +++ /dev/null @@ -1,238 +0,0 @@ - -Add protein lengths from fasta file to data frame (id_col - protein id column.) — add_protein_lengths • prolfqua - - -
-
- - - -
-
-
-

Add protein lengths from fasta file to data frame (id_col - protein id column.)

- Source: R/tidyMS_SaitExpress.R - -
- -
-

Add protein lengths from fasta file to data frame (id_col - protein id column.)

-

Convert tidy table with protein quants into SaintExpress compatible inputs

-

Network visualization. -look at https://www.jessesadler.com/post/network-analysis-with-r/ -https://fgcz-intranet.uzh.ch/tiki-index.php?page=WG_APMSnProximityLabeling

-
- -
- 
add_protein_lengths(intdata, fasta, id_col = "protein_Id")
-
-protein_2localSaint(
-  xx,
-  quantcolumn = "mq.protein.intensity",
-  proteinID = "protein_Id",
-  geneNames = proteinID,
-  proteinLength = "protein.length",
-  IP_name = "raw.file",
-  baitCol = "bait",
-  CorTCol = "CorT"
-)
-
-runSaint(si, filedir = getwd(), spc = TRUE, CLEANUP = TRUE)
-
- -
-

Arguments

-
intdata
-

data.frame

- - -
fasta
-

list of sequences created with read.fasta

- - -
id_col
-

column with protein ids/accessions.

- - -
xx
-

data.frame in long format

- - -
quantcolumn
-

intensity column

- - -
proteinID
-

protein accession

- - -
geneNames
-

column with gene names

- - -
proteinLength
-

column with protein lengths

- - -
IP_name
-

raw.file

- - -
baitCol
-

column with bait definition (condition)

- - -
CorTCol
-

is it control or TRUE (SaintExpress speach)

- - -
si
-

output of protein_2localSaint function

- - -
filedir
-

where to store the saint express inputs

- - -
spc
-

if TRUE spectum counts if FALSE intensities (see SaintExpress documentation for more details)

- - -
CLEANUP
-

TRUE remove all files generated bySaintExpress.

- -
- -
-

Examples

- 

-bb <- prolfqua_data('data_IonstarProtein_subsetNorm')
-bb$config <- old2new(config = bb$config$clone( deep = TRUE))
-xx <- LFQData$new(bb$data, bb$config)
-exampleDat <- xx$data |> dplyr::mutate(CorT = dplyr::case_when(dilution. == "a" ~ "C", TRUE ~ "T"))
-# sample protein lengths
-
-tmp <- data.frame(protein_Id = unique(exampleDat$protein_Id))
-tmp$proteinLength <- as.integer(runif(nrow(tmp), min = 150, max = 2500))
-exampleDat <- dplyr::inner_join(tmp, exampleDat)
-#> Joining with `by = join_by(protein_Id)`
-#undebug(protein_2localSaint)
-res <- protein_2localSaint(exampleDat,quantcolumn = "medpolish",
-                   proteinID = "protein_Id",
-                   proteinLength = "proteinLength",
-                   IP_name = "raw.file",
-                   baitCol = "dilution.",
-                   CorTCol = "CorT"
-                   )
-
-stopifnot(names(res) == c( "inter", "prey",  "bait"))
-if(!Sys.info()["sysname"] == "Darwin") {
-  data_SAINTe_output <- runSaint(res, filedir = tempdir())
-  #usethis::use_data(data_SAINTe_output)
-} else {
- testthat::expect_error(runSaint(res, filedir = tempdir()))
-}
-#> /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/inter.txt
-#> /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/prey.txt
-#> /var/folders/5v/30q3lqxs6_b88gc005sg2t7c0000gn/T//RtmpZERikW/bait.txt
-
-
-
-
- -
- - -
-

Developed by Witold Wolski.

-
- -
-

Site built with pkgdown 2.0.7.

-
- -
- - - - - - - - diff --git a/reference/sim_lfq_data.html b/reference/sim_lfq_data.html index ed2fe1bc0..71c173473 100644 --- a/reference/sim_lfq_data.html +++ b/reference/sim_lfq_data.html @@ -128,16 +128,16 @@

Examples

#> # A tibble: 120 × 11 #> proteinID idtype2 nrPeptides average_prot_abundance sd sample group mean #> <chr> <chr> <dbl> <dbl> <dbl> <chr> <chr> <dbl> -#> 1 P26mFQ 7593 1 18.6 1 Ctrl_V1 Ctrl 0 -#> 2 P26mFQ 7593 1 18.6 1 Ctrl_V2 Ctrl 0 -#> 3 P26mFQ 7593 1 18.6 1 Ctrl_V3 Ctrl 0 -#> 4 P26mFQ 7593 1 18.6 1 Ctrl_V4 Ctrl 0 -#> 5 P26mFQ 7593 1 20.6 1 A_V1 A -2 -#> 6 P26mFQ 7593 1 20.6 1 A_V2 A -2 -#> 7 P26mFQ 7593 1 20.6 1 A_V3 A -2 -#> 8 P26mFQ 7593 1 20.6 1 A_V4 A -2 -#> 9 P26mFQ 7593 1 17.6 1 B_V1 B 1 -#> 10 P26mFQ 7593 1 17.6 1 B_V2 B 1 +#> 1 ZyKS93 2834 5 27.1 1 Ctrl_V1 Ctrl 0 +#> 2 ZyKS93 2834 5 27.1 1 Ctrl_V2 Ctrl 0 +#> 3 ZyKS93 2834 5 27.1 1 Ctrl_V3 Ctrl 0 +#> 4 ZyKS93 2834 5 27.1 1 Ctrl_V4 Ctrl 0 +#> 5 ZyKS93 2834 5 29.1 1 A_V1 A -2 +#> 6 ZyKS93 2834 5 29.1 1 A_V2 A -2 +#> 7 ZyKS93 2834 5 29.1 1 A_V3 A -2 +#> 8 ZyKS93 2834 5 29.1 1 A_V4 A -2 +#> 9 ZyKS93 2834 5 26.1 1 B_V1 B 1 +#> 10 ZyKS93 2834 5 26.1 1 B_V2 B 1 #> # ℹ 110 more rows #> # ℹ 3 more variables: N <dbl>, Replicate <chr>, abundance <dbl> res <- sim_lfq_data(Nprot = 10, PEPTIDE = TRUE) diff --git a/reference/sim_lfq_data_peptide_config.html b/reference/sim_lfq_data_peptide_config.html index a4e48bf72..582d4a8b6 100644 --- a/reference/sim_lfq_data_peptide_config.html +++ b/reference/sim_lfq_data_peptide_config.html @@ -108,6 +108,15 @@

Arguments

+
+

Examples

+ 
x <- sim_lfq_data_peptide_config()
+#> sample already exists
+#> completing cases
+stopifnot("data.frame" %in% class(x$data))
+stopifnot("AnalysisConfiguration" %in% class(x$config))
+
+
+
+

Examples

+ 
x <- sim_lfq_data_protein_config()
+#> sample already exists
+#> completing cases
+stopifnot("data.frame" %in% class(x$data))
+stopifnot("AnalysisConfiguration" %in% class(x$config))
+
+
+
diff --git a/reference/workflow_corr_filter_impute.html b/reference/workflow_corr_filter_impute.html index cd87aa56a..75f1479b5 100644 --- a/reference/workflow_corr_filter_impute.html +++ b/reference/workflow_corr_filter_impute.html @@ -137,7 +137,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 75: `row.names = "NCPHVVVGTPGR"`, `col.names = +#> ℹ In group 75: `row.names = "NCPHVVVGTPGR"` and `col.names = #> "VNIVFNYDMPEDSDTYLHR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -145,14 +145,14 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 21: `row.names = "DMILQFISR"`, `col.names = "RPLILQLIFSK"`. +#> ℹ In group 21: `row.names = "DMILQFISR"` and `col.names = "RPLILQLIFSK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. #> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 125: `row.names = "FMETTDPSTASSLQAK"`, `col.names = +#> ℹ In group 125: `row.names = "FMETTDPSTASSLQAK"` and `col.names = #> "SIDELNSAWDSLNK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -160,7 +160,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 87: `row.names = "KAEAQIAAK"`, `col.names = +#> ℹ In group 87: `row.names = "KAEAQIAAK"` and `col.names = #> "MNLGVGAYRDDNGKPYVLPSVR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -168,7 +168,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 3: `row.names = "DQQNLPYGVTPASPSGHSQGR"`, `col.names = +#> ℹ In group 3: `row.names = "DQQNLPYGVTPASPSGHSQGR"` and `col.names = #> "TTPTPSTNSVLSTSTNR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -176,7 +176,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 3: `row.names = "LLDGFFIRPFYK"`, `col.names = +#> ℹ In group 3: `row.names = "LLDGFFIRPFYK"` and `col.names = #> "RPTPQDNLTDAENGNIQLQAQR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -184,42 +184,44 @@

Examples

#> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 3: `row.names = "MTEWETAAPAVAETPDIK"`, `col.names = "QAVDVSPLRR"`. +#> ℹ In group 3: `row.names = "MTEWETAAPAVAETPDIK"` and `col.names = +#> "QAVDVSPLRR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings. #> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 374: `row.names = "GPLEYVPSAK"`, `col.names = "TAVFGFETSEAK"`. +#> ℹ In group 374: `row.names = "GPLEYVPSAK"` and `col.names = "TAVFGFETSEAK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings. #> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 180: `row.names = "VLPLEEAYR"`, `col.names = "YLLEQDFPGMR"`. +#> ℹ In group 180: `row.names = "VLPLEEAYR"` and `col.names = "YLLEQDFPGMR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. #> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 141: `row.names = "ETAPGDISPYTIPEEDR"`, `col.names = "PVMQALLHIIR"`. +#> ℹ In group 141: `row.names = "ETAPGDISPYTIPEEDR"` and `col.names = +#> "PVMQALLHIIR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. #> Warning: There were 6 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 588: `row.names = "DHRDNLEFFLAGIGR"`, `col.names = "VMGLVPAK"`. +#> ℹ In group 588: `row.names = "DHRDNLEFFLAGIGR"` and `col.names = "VMGLVPAK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 5 remaining warnings. #> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 335: `row.names = "EKLCYVALDFEQEMATAASSSSLEK"`, `col.names = +#> ℹ In group 335: `row.names = "EKLCYVALDFEQEMATAASSSSLEK"` and `col.names = #> "HQGVMVGMGQKDSYVGDEAQSK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -227,7 +229,7 @@

Examples

#> Warning: There were 6 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 32: `row.names = "ALSINTLVK"`, `col.names = "SVPNQPSTNEILQAVLK"`. +#> ℹ In group 32: `row.names = "ALSINTLVK"` and `col.names = "SVPNQPSTNEILQAVLK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 5 remaining warnings. diff --git a/reference/workflow_correlation_preprocessing_protein_intensities.html b/reference/workflow_correlation_preprocessing_protein_intensities.html index 934ab465b..823488628 100644 --- a/reference/workflow_correlation_preprocessing_protein_intensities.html +++ b/reference/workflow_correlation_preprocessing_protein_intensities.html @@ -152,7 +152,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 75: `row.names = "NCPHVVVGTPGR"`, `col.names = +#> ℹ In group 75: `row.names = "NCPHVVVGTPGR"` and `col.names = #> "VNIVFNYDMPEDSDTYLHR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -160,14 +160,14 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 21: `row.names = "DMILQFISR"`, `col.names = "RPLILQLIFSK"`. +#> ℹ In group 21: `row.names = "DMILQFISR"` and `col.names = "RPLILQLIFSK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. #> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 125: `row.names = "FMETTDPSTASSLQAK"`, `col.names = +#> ℹ In group 125: `row.names = "FMETTDPSTASSLQAK"` and `col.names = #> "SIDELNSAWDSLNK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -175,7 +175,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 87: `row.names = "KAEAQIAAK"`, `col.names = +#> ℹ In group 87: `row.names = "KAEAQIAAK"` and `col.names = #> "MNLGVGAYRDDNGKPYVLPSVR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -183,7 +183,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 3: `row.names = "DQQNLPYGVTPASPSGHSQGR"`, `col.names = +#> ℹ In group 3: `row.names = "DQQNLPYGVTPASPSGHSQGR"` and `col.names = #> "TTPTPSTNSVLSTSTNR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -191,7 +191,7 @@

Examples

#> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 3: `row.names = "LLDGFFIRPFYK"`, `col.names = +#> ℹ In group 3: `row.names = "LLDGFFIRPFYK"` and `col.names = #> "RPTPQDNLTDAENGNIQLQAQR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -199,42 +199,44 @@

Examples

#> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 3: `row.names = "MTEWETAAPAVAETPDIK"`, `col.names = "QAVDVSPLRR"`. +#> ℹ In group 3: `row.names = "MTEWETAAPAVAETPDIK"` and `col.names = +#> "QAVDVSPLRR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings. #> Warning: There were 4 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 374: `row.names = "GPLEYVPSAK"`, `col.names = "TAVFGFETSEAK"`. +#> ℹ In group 374: `row.names = "GPLEYVPSAK"` and `col.names = "TAVFGFETSEAK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings. #> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 180: `row.names = "VLPLEEAYR"`, `col.names = "YLLEQDFPGMR"`. +#> ℹ In group 180: `row.names = "VLPLEEAYR"` and `col.names = "YLLEQDFPGMR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. #> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 141: `row.names = "ETAPGDISPYTIPEEDR"`, `col.names = "PVMQALLHIIR"`. +#> ℹ In group 141: `row.names = "ETAPGDISPYTIPEEDR"` and `col.names = +#> "PVMQALLHIIR"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. #> Warning: There were 6 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 588: `row.names = "DHRDNLEFFLAGIGR"`, `col.names = "VMGLVPAK"`. +#> ℹ In group 588: `row.names = "DHRDNLEFFLAGIGR"` and `col.names = "VMGLVPAK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 5 remaining warnings. #> Warning: There were 2 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 335: `row.names = "EKLCYVALDFEQEMATAASSSSLEK"`, `col.names = +#> ℹ In group 335: `row.names = "EKLCYVALDFEQEMATAASSSSLEK"` and `col.names = #> "HQGVMVGMGQKDSYVGDEAQSK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf @@ -242,7 +244,7 @@

Examples

#> Warning: There were 6 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `jcor = (function (x) ...`. -#> ℹ In group 32: `row.names = "ALSINTLVK"`, `col.names = "SVPNQPSTNEILQAVLK"`. +#> ℹ In group 32: `row.names = "ALSINTLVK"` and `col.names = "SVPNQPSTNEILQAVLK"`. #> Caused by warning in `max()`: #> ! no non-missing arguments to max; returning -Inf #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 5 remaining warnings. diff --git a/sitemap.xml b/sitemap.xml index 905529dd1..b1e9779f4 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -579,9 +579,6 @@ /reference/robust_scale.html - - /reference/saintExpress.html - /reference/sample_subset.html