diff --git a/404.html b/404.html index b396f423..83f92069 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index dab82f58..50a20e42 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 7abfeb60..dc498edc 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/LICENSE.html b/LICENSE.html index a4a55d40..be42ad9b 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/articles/Comparing2Groups.html b/articles/Comparing2Groups.html index b42e026b..126a54e5 100644 --- a/articles/Comparing2Groups.html +++ b/articles/Comparing2Groups.html @@ -33,7 +33,7 @@ prolfqua - 1.2.4 + 1.2.5 @@ -100,7 +100,7 @@

Comparing Two Groups with prolfqua

Witold E. Wolski

-

2024-05-21

+

2024-05-22

Source: vignettes/Comparing2Groups.Rmd @@ -448,7 +448,7 @@

Compute contrastsplotter$ma_plotly()
-

+

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

@@ -568,7 +568,7 @@

Session Info## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: -## [1] prolfqua_1.2.4 +## [1] prolfqua_1.2.5 ## ## loaded via a namespace (and not attached): ## [1] gtable_0.3.5 xfun_0.43 bslib_0.7.0 ggplot2_3.5.1 diff --git a/articles/CreatingConfigurations.html b/articles/CreatingConfigurations.html index fea532d4..af6e4eac 100644 --- a/articles/CreatingConfigurations.html +++ b/articles/CreatingConfigurations.html @@ -33,7 +33,7 @@ prolfqua - 1.2.4 + 1.2.5

@@ -97,7 +97,7 @@

Creating prolfqua Configurations

Witold E. Wolski

-

2024-05-21

+

2024-05-22

Source: vignettes/CreatingConfigurations.Rmd @@ -312,7 +312,7 @@

Session Info## [1] plotly_4.10.4 sass_0.4.9 utf8_1.2.4 generics_0.1.3 ## [5] tidyr_1.3.1 stringi_1.8.3 digest_0.6.35 magrittr_2.0.3 ## [9] evaluate_0.23 grid_4.3.2 RColorBrewer_1.1-3 fastmap_1.1.1 -## [13] jsonlite_1.8.8 ggrepel_0.9.5 prolfqua_1.2.4 conflicted_1.2.0 +## [13] jsonlite_1.8.8 ggrepel_0.9.5 prolfqua_1.2.5 conflicted_1.2.0 ## [17] gridExtra_2.3 httr_1.4.7 purrr_1.0.2 fansi_1.0.6 ## [21] viridisLite_0.4.2 scales_1.3.0 lazyeval_0.2.2 textshaping_0.3.7 ## [25] jquerylib_0.1.4 cli_3.6.2 rlang_1.1.3 munsell_0.5.1 diff --git a/articles/Modelling2Factors.html b/articles/Modelling2Factors.html index 7fc65f4b..41f6b7c2 100644 --- a/articles/Modelling2Factors.html +++ b/articles/Modelling2Factors.html @@ -33,7 +33,7 @@ prolfqua - 1.2.4 + 1.2.5 @@ -97,7 +97,7 @@

Modelling dataset with two Factors

Witold E. Wolski

-

2024-05-21

+

2024-05-22

Source: vignettes/Modelling2Factors.Rmd @@ -388,6 +388,11 @@

Alternative model specification

+

Likelihood ratio Test for models with more factors +

+

TODO. Introduce Likelihood ratio test

+
+

Testing interaction computation

@@ -419,7 +424,7 @@

Session Info## [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_1.15.4 RColorBrewer_1.1-3 desc_1.4.3 lifecycle_1.0.4 -## [21] prolfqua_1.2.4 compiler_4.3.2 farver_2.1.1 stringr_1.5.1 +## [21] prolfqua_1.2.5 compiler_4.3.2 farver_2.1.1 stringr_1.5.1 ## [25] textshaping_0.3.7 progress_1.2.3 munsell_0.5.1 carData_3.0-5 ## [29] vipor_0.4.7 htmltools_0.5.8.1 sass_0.4.9 yaml_2.3.8 ## [33] lazyeval_0.2.2 plotly_4.10.4 car_3.1-2 pillar_1.9.0 diff --git a/articles/QCandSampleSize.html b/articles/QCandSampleSize.html index a1f69224..ad91f91f 100644 --- a/articles/QCandSampleSize.html +++ b/articles/QCandSampleSize.html @@ -33,7 +33,7 @@ prolfqua - 1.2.4 + 1.2.5 @@ -98,7 +98,7 @@

Quality Control & Sample Size

Witold Wolski

-

21 May, 2024

+

22 May, 2024

Source: vignettes/QCandSampleSize.Rmd diff --git a/articles/QualityControlAndSampleSizeEstimation.html b/articles/QualityControlAndSampleSizeEstimation.html index be6a1618..efb0e257 100644 --- a/articles/QualityControlAndSampleSizeEstimation.html +++ b/articles/QualityControlAndSampleSizeEstimation.html @@ -33,7 +33,7 @@ prolfqua - 1.2.4 + 1.2.5 @@ -97,7 +97,7 @@

QC and Sample Size Estimation

Witold E. Wolski

-

2024-05-21

+

2024-05-22

Source: vignettes/QualityControlAndSampleSizeEstimation.Rmd @@ -817,7 +817,7 @@

Session Info## [5] generics_0.1.3 KernSmooth_2.23-22 lattice_0.22-5 stringi_1.8.3 ## [9] digest_0.6.35 magrittr_2.0.3 evaluate_0.23 grid_4.3.2 ## [13] RColorBrewer_1.1-3 fastmap_1.1.1 Matrix_1.6-5 jsonlite_1.8.8 -## [17] ggrepel_0.9.5 prolfqua_1.2.4 conflicted_1.2.0 gridExtra_2.3 +## [17] ggrepel_0.9.5 prolfqua_1.2.5 conflicted_1.2.0 gridExtra_2.3 ## [21] mgcv_1.9-1 httr_1.4.7 purrr_1.0.2 fansi_1.0.6 ## [25] viridisLite_0.4.2 scales_1.3.0 lazyeval_0.2.2 textshaping_0.3.7 ## [29] jquerylib_0.1.4 cli_3.6.2 rlang_1.1.3 splines_4.3.2 diff --git a/articles/SimulateData.html b/articles/SimulateData.html index d992e0b9..84a74780 100644 --- a/articles/SimulateData.html +++ b/articles/SimulateData.html @@ -33,7 +33,7 @@ prolfqua - 1.2.4 + 1.2.5 @@ -97,7 +97,7 @@

Simulate Peptide level Data

Witold E. Wolski

-

2024-05-21

+

2024-05-22

Source: vignettes/SimulateData.Rmd diff --git a/articles/TestingMissingInference.html b/articles/TestingMissingInference.html index 3fe2f582..c2f05143 100644 --- a/articles/TestingMissingInference.html +++ b/articles/TestingMissingInference.html @@ -33,7 +33,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/articles/index.html b/articles/index.html index 61654dcf..8d1774cd 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/authors.html b/authors.html index e34f9155..2dd1f4fb 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/index.html b/index.html index aa6bda0f..31285232 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ prolfqua - 1.2.4 + 1.2.5 @@ -135,7 +135,7 @@

How to get started## read MQ peptide.txt and annotation table startdata <- prolfqua::tidyMQ_Peptides(system.file( "samples/maxquant_txt/tiny2.zip", package = "prolfqua")) -annot <- readxl::read_xlsx(system.file( +annot <- readxl::read_xlsx(system.file( "samples/maxquant_txt/annotation_Ionstar2018_PXD003881.xlsx", package = "prolfqua")) startdata <- dplyr::inner_join(annot, startdata, by = "raw.file") diff --git a/pkgdown.yml b/pkgdown.yml index a88541df..bca6db0b 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -9,5 +9,5 @@ articles: QualityControlAndSampleSizeEstimation: QualityControlAndSampleSizeEstimation.html SimulateData: SimulateData.html TestingMissingInference: TestingMissingInference.html -last_built: 2024-05-21T18:34Z +last_built: 2024-05-21T21:36Z diff --git a/reference/AnalysisConfiguration.html b/reference/AnalysisConfiguration.html index 30c79969..efc279bb 100644 --- a/reference/AnalysisConfiguration.html +++ b/reference/AnalysisConfiguration.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/AnalysisParameters.html b/reference/AnalysisParameters.html index be37be1e..264f743d 100644 --- a/reference/AnalysisParameters.html +++ b/reference/AnalysisParameters.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/AnalysisTableAnnotation.html b/reference/AnalysisTableAnnotation.html index 19a001b5..ed4a1e27 100644 --- a/reference/AnalysisTableAnnotation.html +++ b/reference/AnalysisTableAnnotation.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/Benchmark.html b/reference/Benchmark.html index 1c91b8a0..94c39c64 100644 --- a/reference/Benchmark.html +++ b/reference/Benchmark.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/Contrasts.html b/reference/Contrasts.html index 4c4d0007..a7e88bb0 100644 --- a/reference/Contrasts.html +++ b/reference/Contrasts.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/ContrastsInterface.html b/reference/ContrastsInterface.html index 3cd4204f..1d74ad10 100644 --- a/reference/ContrastsInterface.html +++ b/reference/ContrastsInterface.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/ContrastsMissing.html b/reference/ContrastsMissing.html index 7a079e02..74394065 100644 --- a/reference/ContrastsMissing.html +++ b/reference/ContrastsMissing.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/ContrastsModerated.html b/reference/ContrastsModerated.html index 5f515e2c..8499d219 100644 --- a/reference/ContrastsModerated.html +++ b/reference/ContrastsModerated.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/ContrastsPlotter.html b/reference/ContrastsPlotter.html index 57b71b4c..be7ed6f5 100644 --- a/reference/ContrastsPlotter.html +++ b/reference/ContrastsPlotter.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/ContrastsProDA.html b/reference/ContrastsProDA.html index 8df2c3a2..79929a75 100644 --- a/reference/ContrastsProDA.html +++ b/reference/ContrastsProDA.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/ContrastsROPECA.html b/reference/ContrastsROPECA.html index 2a2f623a..ecf5d2ef 100644 --- a/reference/ContrastsROPECA.html +++ b/reference/ContrastsROPECA.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/ContrastsTable.html b/reference/ContrastsTable.html index 4a1f734d..923bc19c 100644 --- a/reference/ContrastsTable.html +++ b/reference/ContrastsTable.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/INTERNAL_FUNCTIONS_BY_FAMILY.html b/reference/INTERNAL_FUNCTIONS_BY_FAMILY.html index 169d5dc8..aff4e367 100644 --- a/reference/INTERNAL_FUNCTIONS_BY_FAMILY.html +++ b/reference/INTERNAL_FUNCTIONS_BY_FAMILY.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/LFQData.html b/reference/LFQData.html index 2796ad09..7648a1f9 100644 --- a/reference/LFQData.html +++ b/reference/LFQData.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/LFQDataAggregator.html b/reference/LFQDataAggregator.html index 512fa3c3..2d7a08a5 100644 --- a/reference/LFQDataAggregator.html +++ b/reference/LFQDataAggregator.html @@ -20,7 +20,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/LFQDataPlotter.html b/reference/LFQDataPlotter.html index 63041ae6..d6aceaaa 100644 --- a/reference/LFQDataPlotter.html +++ b/reference/LFQDataPlotter.html @@ -20,7 +20,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/LFQDataStats.html b/reference/LFQDataStats.html index 763b5f0a..080fc5d9 100644 --- a/reference/LFQDataStats.html +++ b/reference/LFQDataStats.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/LFQDataSummariser.html b/reference/LFQDataSummariser.html index aa72b53e..d804a203 100644 --- a/reference/LFQDataSummariser.html +++ b/reference/LFQDataSummariser.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/LFQDataToSummarizedExperiment.html b/reference/LFQDataToSummarizedExperiment.html index d6381a8f..1fbef658 100644 --- a/reference/LFQDataToSummarizedExperiment.html +++ b/reference/LFQDataToSummarizedExperiment.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/LFQDataTransformer.html b/reference/LFQDataTransformer.html index 69c99af1..85d56292 100644 --- a/reference/LFQDataTransformer.html +++ b/reference/LFQDataTransformer.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/LFQDataWriter.html b/reference/LFQDataWriter.html index 0cffe9b6..1c11c8a1 100644 --- a/reference/LFQDataWriter.html +++ b/reference/LFQDataWriter.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/LR_test.html b/reference/LR_test.html index bc65468f..124c1ae4 100644 --- a/reference/LR_test.html +++ b/reference/LR_test.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/MissingHelpers.html b/reference/MissingHelpers.html index 6ea95e83..8f4b4e67 100644 --- a/reference/MissingHelpers.html +++ b/reference/MissingHelpers.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/Model.html b/reference/Model.html index 5faf4dd9..223502f7 100644 --- a/reference/Model.html +++ b/reference/Model.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/ModelInterface.html b/reference/ModelInterface.html index 4e2cc9a5..eeef1937 100644 --- a/reference/ModelInterface.html +++ b/reference/ModelInterface.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/PACKAGE_DATA.html b/reference/PACKAGE_DATA.html index 07b08f8c..fbe85a5c 100644 --- a/reference/PACKAGE_DATA.html +++ b/reference/PACKAGE_DATA.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/ProjectStructure.html b/reference/ProjectStructure.html index 07e552e5..ed607bc5 100644 --- a/reference/ProjectStructure.html +++ b/reference/ProjectStructure.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/ProteinAnnotation.html b/reference/ProteinAnnotation.html index c587d8a8..acd7f73b 100644 --- a/reference/ProteinAnnotation.html +++ b/reference/ProteinAnnotation.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/R6_extract_values.html b/reference/R6_extract_values.html index 47c2bce0..3456983b 100644 --- a/reference/R6_extract_values.html +++ b/reference/R6_extract_values.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/UpSet_interaction_missing_stats.html b/reference/UpSet_interaction_missing_stats.html index 659f5e3a..d42e346e 100644 --- a/reference/UpSet_interaction_missing_stats.html +++ b/reference/UpSet_interaction_missing_stats.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/UpSet_missing_stats.html b/reference/UpSet_missing_stats.html index 7342c504..3d3da117 100644 --- a/reference/UpSet_missing_stats.html +++ b/reference/UpSet_missing_stats.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/adjust_p_values.html b/reference/adjust_p_values.html index 8ea79c6c..267bb4f7 100644 --- a/reference/adjust_p_values.html +++ b/reference/adjust_p_values.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/aggregate_intensity_topN.html b/reference/aggregate_intensity_topN.html index 79c080e6..fc842488 100644 --- a/reference/aggregate_intensity_topN.html +++ b/reference/aggregate_intensity_topN.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/apply_to_response_matrix.html b/reference/apply_to_response_matrix.html index 95502bc6..b8b5b0ff 100644 --- a/reference/apply_to_response_matrix.html +++ b/reference/apply_to_response_matrix.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/build_model.html b/reference/build_model.html index 30cdb0ac..df88fef8 100644 --- a/reference/build_model.html +++ b/reference/build_model.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/complete_cases.html b/reference/complete_cases.html index 12cb47b2..402bd30c 100644 --- a/reference/complete_cases.html +++ b/reference/complete_cases.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/concrete_AnalysisConfiguration.html b/reference/concrete_AnalysisConfiguration.html index f3f560ac..0517a802 100644 --- a/reference/concrete_AnalysisConfiguration.html +++ b/reference/concrete_AnalysisConfiguration.html @@ -19,7 +19,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/contrasts_fisher_exact.html b/reference/contrasts_fisher_exact.html index 025e8d01..5130ee26 100644 --- a/reference/contrasts_fisher_exact.html +++ b/reference/contrasts_fisher_exact.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/contrasts_linfct.html b/reference/contrasts_linfct.html index 272b36a1..fdd47c01 100644 --- a/reference/contrasts_linfct.html +++ b/reference/contrasts_linfct.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/cor_jackknife_matrix.html b/reference/cor_jackknife_matrix.html index 5a783327..7fa18e4f 100644 --- a/reference/cor_jackknife_matrix.html +++ b/reference/cor_jackknife_matrix.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/cor_order.html b/reference/cor_order.html index 56daffa7..d92f179c 100644 --- a/reference/cor_order.html +++ b/reference/cor_order.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_IonstarProtein_subsetNorm.html b/reference/data_IonstarProtein_subsetNorm.html index 6347dfcf..1ea7aa57 100644 --- a/reference/data_IonstarProtein_subsetNorm.html +++ b/reference/data_IonstarProtein_subsetNorm.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_SAINTe_output.html b/reference/data_SAINTe_output.html index c924e4be..3c03f4bb 100644 --- a/reference/data_SAINTe_output.html +++ b/reference/data_SAINTe_output.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_basicModel_p1807.html b/reference/data_basicModel_p1807.html index 8a1fe2d2..6803dd28 100644 --- a/reference/data_basicModel_p1807.html +++ b/reference/data_basicModel_p1807.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_benchmarkExample.html b/reference/data_benchmarkExample.html index 959ccd73..8ac9aad5 100644 --- a/reference/data_benchmarkExample.html +++ b/reference/data_benchmarkExample.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_checksummarizationrobust87.html b/reference/data_checksummarizationrobust87.html index dff4d12c..be5dd70b 100644 --- a/reference/data_checksummarizationrobust87.html +++ b/reference/data_checksummarizationrobust87.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_checksummarizerobust.html b/reference/data_checksummarizerobust.html index 70c49531..bfeaa0b3 100644 --- a/reference/data_checksummarizerobust.html +++ b/reference/data_checksummarizerobust.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_checksummarizerobust69.html b/reference/data_checksummarizerobust69.html index d2a4fbc6..2949b34d 100644 --- a/reference/data_checksummarizerobust69.html +++ b/reference/data_checksummarizerobust69.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_correlatedPeptideList.html b/reference/data_correlatedPeptideList.html index 61e384c5..db2b7a45 100644 --- a/reference/data_correlatedPeptideList.html +++ b/reference/data_correlatedPeptideList.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_interactionModel_p1807.html b/reference/data_interactionModel_p1807.html index 2e3f5b09..c8f88e3e 100644 --- a/reference/data_interactionModel_p1807.html +++ b/reference/data_interactionModel_p1807.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_ionstar.html b/reference/data_ionstar.html index fdb73d93..e32c7a26 100644 --- a/reference/data_ionstar.html +++ b/reference/data_ionstar.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_multigroupFC.html b/reference/data_multigroupFC.html index b57bf274..0d7c9278 100644 --- a/reference/data_multigroupFC.html +++ b/reference/data_multigroupFC.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_skylinePRMSample_A.html b/reference/data_skylinePRMSample_A.html index db3313c7..5047d728 100644 --- a/reference/data_skylinePRMSample_A.html +++ b/reference/data_skylinePRMSample_A.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/data_skylineSRM_HL_A.html b/reference/data_skylineSRM_HL_A.html index f32a0f3e..ec5df224 100644 --- a/reference/data_skylineSRM_HL_A.html +++ b/reference/data_skylineSRM_HL_A.html @@ -17,7 +17,7 @@ prolfqua - 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1.2.4 + 1.2.5 diff --git a/reference/panel_cor.html b/reference/panel_cor.html index ac45cdd4..5208f6f5 100644 --- a/reference/panel_cor.html +++ b/reference/panel_cor.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/panel_hist.html b/reference/panel_hist.html index 20646d75..01ec4c1c 100644 --- a/reference/panel_hist.html +++ b/reference/panel_hist.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/pivot_model_contrasts_2_Wide.html b/reference/pivot_model_contrasts_2_Wide.html index 6777bc42..c5fec14e 100644 --- a/reference/pivot_model_contrasts_2_Wide.html +++ b/reference/pivot_model_contrasts_2_Wide.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_NA_heatmap.html b/reference/plot_NA_heatmap.html index fc3fa239..0a67c597 100644 --- a/reference/plot_NA_heatmap.html +++ b/reference/plot_NA_heatmap.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_estimate.html b/reference/plot_estimate.html index 7e7fba8f..843ea038 100644 --- a/reference/plot_estimate.html +++ b/reference/plot_estimate.html @@ -17,7 +17,7 @@ prolfqua - 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1.2.4 + 1.2.5 diff --git a/reference/plot_hierarchies_line.html b/reference/plot_hierarchies_line.html index 9a149190..a9de9762 100644 --- a/reference/plot_hierarchies_line.html +++ b/reference/plot_hierarchies_line.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_hierarchies_line_df.html b/reference/plot_hierarchies_line_df.html index ce804e4c..fdc12316 100644 --- a/reference/plot_hierarchies_line_df.html +++ b/reference/plot_hierarchies_line_df.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_intensity_distribution_violin.html b/reference/plot_intensity_distribution_violin.html index b8fb1cca..761f761c 100644 --- a/reference/plot_intensity_distribution_violin.html +++ b/reference/plot_intensity_distribution_violin.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_lmer_peptide_predictions.html b/reference/plot_lmer_peptide_predictions.html index b69d5380..4c7df0a1 100644 --- a/reference/plot_lmer_peptide_predictions.html +++ b/reference/plot_lmer_peptide_predictions.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_pca.html b/reference/plot_pca.html index 59372dee..7bd4cb55 100644 --- a/reference/plot_pca.html +++ b/reference/plot_pca.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_raster.html b/reference/plot_raster.html index 97d3cdaf..d57a6580 100644 --- a/reference/plot_raster.html +++ b/reference/plot_raster.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_sample_correlation.html b/reference/plot_sample_correlation.html index 0a20e202..87973931 100644 --- a/reference/plot_sample_correlation.html +++ b/reference/plot_sample_correlation.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_screeplot.html b/reference/plot_screeplot.html index 15ad676b..10ccf2df 100644 --- a/reference/plot_screeplot.html +++ b/reference/plot_screeplot.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_stat_density.html b/reference/plot_stat_density.html index 64dede00..456d490e 100644 --- a/reference/plot_stat_density.html +++ b/reference/plot_stat_density.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_stat_density_median.html b/reference/plot_stat_density_median.html index 6e577043..ec6e7c48 100644 --- a/reference/plot_stat_density_median.html +++ b/reference/plot_stat_density_median.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_stat_violin.html b/reference/plot_stat_violin.html index 7740472b..238ec4f8 100644 --- a/reference/plot_stat_violin.html +++ b/reference/plot_stat_violin.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_stat_violin_median.html b/reference/plot_stat_violin_median.html index b87a76a3..8893ac72 100644 --- a/reference/plot_stat_violin_median.html +++ b/reference/plot_stat_violin_median.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/plot_stdv_vs_mean.html b/reference/plot_stdv_vs_mean.html index ae2f0e42..15a8999a 100644 --- a/reference/plot_stdv_vs_mean.html +++ b/reference/plot_stdv_vs_mean.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/pooled_var.html b/reference/pooled_var.html index 9833fea3..81ebc86e 100644 --- a/reference/pooled_var.html +++ b/reference/pooled_var.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/prolfqua_data.html b/reference/prolfqua_data.html index 95ed3d6d..506b22af 100644 --- a/reference/prolfqua_data.html +++ b/reference/prolfqua_data.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/rank_by_NA.html b/reference/rank_by_NA.html index de669672..97e547c7 100644 --- a/reference/rank_by_NA.html +++ b/reference/rank_by_NA.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/rank_peptide_by_intensity.html b/reference/rank_peptide_by_intensity.html index f0fd0bd8..27638c15 100644 --- a/reference/rank_peptide_by_intensity.html +++ b/reference/rank_peptide_by_intensity.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/remove_NA_rows.html b/reference/remove_NA_rows.html index 21c6cab2..70a03a34 100644 --- a/reference/remove_NA_rows.html +++ b/reference/remove_NA_rows.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/remove_large_QValues.html b/reference/remove_large_QValues.html index fc62e88e..6068552a 100644 --- a/reference/remove_large_QValues.html +++ b/reference/remove_large_QValues.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/remove_small_intensities.html b/reference/remove_small_intensities.html index db2bf7e1..49eac533 100644 --- a/reference/remove_small_intensities.html +++ b/reference/remove_small_intensities.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/render_MQSummary_rmd.html b/reference/render_MQSummary_rmd.html index 990f0d22..62094722 100644 --- a/reference/render_MQSummary_rmd.html +++ b/reference/render_MQSummary_rmd.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/response_as_matrix.html b/reference/response_as_matrix.html index 23b4e16a..f942556b 100644 --- a/reference/response_as_matrix.html +++ b/reference/response_as_matrix.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/response_matrix_as_tibble.html b/reference/response_matrix_as_tibble.html index 6f2d55d2..bac59d63 100644 --- a/reference/response_matrix_as_tibble.html +++ b/reference/response_matrix_as_tibble.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/rlm_estimate.html b/reference/rlm_estimate.html index c7157948..fbd3d9d6 100644 --- a/reference/rlm_estimate.html +++ b/reference/rlm_estimate.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/rlm_estimate_dfconfig.html b/reference/rlm_estimate_dfconfig.html index a39149d0..8bb14f3d 100644 --- a/reference/rlm_estimate_dfconfig.html +++ b/reference/rlm_estimate_dfconfig.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/robust_scale.html b/reference/robust_scale.html index 6b0d12f4..7e8112fe 100644 --- a/reference/robust_scale.html +++ b/reference/robust_scale.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/sample_subset.html b/reference/sample_subset.html index 3aac7f38..af7a3ca2 100644 --- a/reference/sample_subset.html +++ b/reference/sample_subset.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/scale_with_subset.html b/reference/scale_with_subset.html index 33581f43..d2a52fc6 100644 --- a/reference/scale_with_subset.html +++ b/reference/scale_with_subset.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/scale_with_subset_by_factors.html b/reference/scale_with_subset_by_factors.html index 92e7d67f..6ded6e33 100644 --- a/reference/scale_with_subset_by_factors.html +++ b/reference/scale_with_subset_by_factors.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/scriptCopyHelperVec.html b/reference/scriptCopyHelperVec.html index 7198be2f..770ca0c2 100644 --- a/reference/scriptCopyHelperVec.html +++ b/reference/scriptCopyHelperVec.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/separate_factors.html b/reference/separate_factors.html index 392da03f..ef618793 100644 --- a/reference/separate_factors.html +++ b/reference/separate_factors.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/separate_hierarchy.html b/reference/separate_hierarchy.html index 26fdb75a..8c5ebe53 100644 --- a/reference/separate_hierarchy.html +++ b/reference/separate_hierarchy.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/setup_analysis.html b/reference/setup_analysis.html index e39c8286..81e8b109 100644 --- a/reference/setup_analysis.html +++ b/reference/setup_analysis.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/sim_build_models_lm.html b/reference/sim_build_models_lm.html index ef3883cf..18fdde80 100644 --- a/reference/sim_build_models_lm.html +++ b/reference/sim_build_models_lm.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/sim_build_models_lmer.html b/reference/sim_build_models_lmer.html index fd0a0812..bdcf775e 100644 --- a/reference/sim_build_models_lmer.html +++ b/reference/sim_build_models_lmer.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/sim_lfq_data.html b/reference/sim_lfq_data.html index 0bc480b9..e6cb8d11 100644 --- a/reference/sim_lfq_data.html +++ b/reference/sim_lfq_data.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/sim_lfq_data_2Factor_config.html b/reference/sim_lfq_data_2Factor_config.html index f3afe425..d4f2ff60 100644 --- a/reference/sim_lfq_data_2Factor_config.html +++ b/reference/sim_lfq_data_2Factor_config.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/sim_lfq_data_peptide_config.html b/reference/sim_lfq_data_peptide_config.html index 88cfbf91..3b4ec062 100644 --- a/reference/sim_lfq_data_peptide_config.html +++ b/reference/sim_lfq_data_peptide_config.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/sim_lfq_data_protein_config.html b/reference/sim_lfq_data_protein_config.html index 40f914ca..23282a46 100644 --- a/reference/sim_lfq_data_protein_config.html +++ b/reference/sim_lfq_data_protein_config.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/sim_make_model_lm.html b/reference/sim_make_model_lm.html index 853dcd99..06d24635 100644 --- a/reference/sim_make_model_lm.html +++ b/reference/sim_make_model_lm.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/sim_make_model_lmer.html b/reference/sim_make_model_lmer.html index 6510441a..908bf37d 100644 --- a/reference/sim_make_model_lmer.html +++ b/reference/sim_make_model_lmer.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/spread_response_by_IsotopeLabel.html b/reference/spread_response_by_IsotopeLabel.html index 5386c946..c86e8eea 100644 --- a/reference/spread_response_by_IsotopeLabel.html +++ b/reference/spread_response_by_IsotopeLabel.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/squeezeVarRob.html b/reference/squeezeVarRob.html index 8b589e01..6c30b26e 100644 --- a/reference/squeezeVarRob.html +++ b/reference/squeezeVarRob.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/strategy.html b/reference/strategy.html index c3e81f1c..d262741c 100644 --- a/reference/strategy.html +++ b/reference/strategy.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 @@ -349,7 +349,7 @@

Examples

tmp <- strategy_lm("Intensity ~ condition", model_name = "parallel design") tmp$model_fun(get_formula = TRUE) #> Intensity ~ condition -#> <environment: 0x30482f510> +#> <environment: 0x17fb9ffe0> tmp$isSingular #> function(m){ #> anyNA <- any(is.na(coefficients(m))) @@ -366,7 +366,7 @@

Examples

tmp <- strategy_rlm("Intensity ~ condition", model_name = "parallel design") tmp$model_fun(get_formula = TRUE) #> Intensity ~ condition -#> <environment: 0x16ed488a0> +#> <environment: 0x36701a038> tmp$isSingular #> function(m){ #> anyNA <- any(is.na(coefficients(m))) @@ -383,7 +383,7 @@

Examples

tmp <- strategy_glm("Intensity ~ condition", model_name = "parallel design") tmp$model_fun(get_formula = TRUE) #> Intensity ~ condition -#> <environment: 0x3028e1040> +#> <environment: 0x36710ee80> tmp$isSingular #> function(m){ #> anyNA <- any(is.na(coefficients(m))) diff --git a/reference/summarise_QValues.html b/reference/summarise_QValues.html index 139703be..5b163093 100644 --- a/reference/summarise_QValues.html +++ b/reference/summarise_QValues.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/summarize_hierarchy.html b/reference/summarize_hierarchy.html index d22ce825..41e706e2 100644 --- a/reference/summarize_hierarchy.html +++ b/reference/summarize_hierarchy.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/summarize_stats.html b/reference/summarize_stats.html index 1bb326b8..209f14b7 100644 --- a/reference/summarize_stats.html +++ b/reference/summarize_stats.html @@ -19,7 +19,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/summarize_stats_factors.html b/reference/summarize_stats_factors.html index 73613f5e..83c051a5 100644 --- a/reference/summarize_stats_factors.html +++ b/reference/summarize_stats_factors.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/summary_ROPECA_median_p.scaled.html b/reference/summary_ROPECA_median_p.scaled.html index bd99af3f..1bf54ae8 100644 --- a/reference/summary_ROPECA_median_p.scaled.html +++ b/reference/summary_ROPECA_median_p.scaled.html @@ -18,7 +18,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/table_facade.html b/reference/table_facade.html index 4d8cfe4d..dbbb5e34 100644 --- a/reference/table_facade.html +++ b/reference/table_facade.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/table_factors.html b/reference/table_factors.html index 5cd18122..77548660 100644 --- a/reference/table_factors.html +++ b/reference/table_factors.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/tidy_to_wide.html b/reference/tidy_to_wide.html index 4a767d81..a44a004a 100644 --- a/reference/tidy_to_wide.html +++ b/reference/tidy_to_wide.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/tidy_to_wide_config.html b/reference/tidy_to_wide_config.html index dd5feab7..87948698 100644 --- a/reference/tidy_to_wide_config.html +++ b/reference/tidy_to_wide_config.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/transform_work_intensity.html b/reference/transform_work_intensity.html index 489add81..ae1e3b35 100644 --- a/reference/transform_work_intensity.html +++ b/reference/transform_work_intensity.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5 diff --git a/reference/which_missing.html b/reference/which_missing.html index 216b12ec..7d23b98c 100644 --- a/reference/which_missing.html +++ b/reference/which_missing.html @@ -17,7 +17,7 @@ prolfqua - 1.2.4 + 1.2.5