diff --git a/articles/MultiEWCE.html b/articles/MultiEWCE.html index 36da533..52e3c27 100644 --- a/articles/MultiEWCE.html +++ b/articles/MultiEWCE.html @@ -89,7 +89,7 @@


-Vignette updated: Nov-09-2023
+Vignette updated: Nov-14-2023

Source: vignettes/MultiEWCE.Rmd @@ -330,14 +330,14 @@

Run analysis## Gene table with 62,663 rows retrieved. 
## Returning all 62,663 genes from human.
## Returning 62,663 unique genes from entire human genome.
-
## + Version: 2023-11-09
+
## + Version: 2023-11-14
## Background contains 62,663 genes.
## Computing gene counts.
 ## Computing gene counts.
 ## Computing gene counts.
-
## Done in: 11.7 seconds.
+
## Done in: 68.5 seconds.
## 
-## Saving results ==> /tmp/Rtmp7Ao7aO/gen_results.rds
+## Saving results ==> /tmp/RtmpXS0WUt/gen_results.rds

Visualise the results @@ -447,16 +447,16 @@

Run disease-level enrichment tests## Gene table with 62,663 rows retrieved. 
## Returning all 62,663 genes from human.
## Returning 62,663 unique genes from entire human genome.
-
## + Version: 2023-11-09
+
## + Version: 2023-11-14
## Background contains 62,663 genes.
## Computing gene counts.
 ## Computing gene counts.
 ## Computing gene counts.
 ## Computing gene counts.
 ## Computing gene counts.
-
## Done in: 13.2 seconds.
+
## Done in: 104.9 seconds.
## 
-## Saving results ==> /tmp/Rtmp7Ao7aO/gen_results.rds
+## Saving results ==> /tmp/RtmpXS0WUt/gen_results.rds

Full analysis @@ -481,7 +481,7 @@

Session info
 utils::sessionInfo()

-
## R Under development (unstable) (2023-11-02 r85465)
+
## R Under development (unstable) (2023-11-08 r85496)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.3 LTS
 ## 
@@ -511,7 +511,7 @@ 
Session info##   [3] ggplotify_0.1.2               GeneOverlap_1.39.0           
 ##   [5] filelock_1.0.2                tibble_3.2.1                 
 ##   [7] ontologyPlot_1.6              ggnetwork_0.5.12             
-##   [9] graph_1.81.0                  httr2_0.2.3                  
+##   [9] graph_1.81.0                  httr2_1.0.0                  
 ##  [11] lifecycle_1.0.4               rstatix_0.7.2                
 ##  [13] HPOExplorer_0.99.12           rprojroot_2.0.4              
 ##  [15] lattice_0.22-5                backports_1.4.1              
@@ -538,7 +538,7 @@ 
Session info##  [57] treeio_1.27.0                 ragg_1.2.6                   
 ##  [59] Rcpp_1.0.11                   glue_1.6.2                   
 ##  [61] SparseArray_1.3.1             xfun_0.41                    
-##  [63] MatrixGenerics_1.15.0         GenomeInfoDb_1.39.0          
+##  [63] MatrixGenerics_1.15.0         GenomeInfoDb_1.39.1          
 ##  [65] RNOmni_1.0.1.2                dplyr_1.1.3                  
 ##  [67] withr_2.5.2                   BiocManager_1.30.22          
 ##  [69] fastmap_1.1.1                 fansi_1.0.5                  
@@ -574,13 +574,13 @@ 
Session info## [129] grr_0.9.5                     ggsignif_0.6.4               
 ## [131] labeling_0.4.3                gprofiler2_0.2.2             
 ## [133] EWCE_1.11.2                   plyr_1.8.9                   
-## [135] fs_1.6.3                      stringi_1.7.12               
+## [135] fs_1.6.3                      stringi_1.8.1                
 ## [137] BiocParallel_1.37.0           viridisLite_0.4.2            
 ## [139] ewceData_1.11.0               network_1.18.1               
 ## [141] babelgene_22.9                munsell_0.5.0                
 ## [143] Biostrings_2.71.1             gh_1.4.0                     
 ## [145] lazyeval_0.2.2                homologene_1.4.68.19.3.27    
-## [147] Matrix_1.6-1.1                ExperimentHub_2.11.0         
+## [147] Matrix_1.6-2                  ExperimentHub_2.11.0         
 ## [149] patchwork_1.1.3               bit64_4.0.5                  
 ## [151] KEGGREST_1.43.0               statmod_1.5.0                
 ## [153] shiny_1.7.5.1                 highr_0.10                   
diff --git a/articles/MultiEWCE_files/figure-html/display-1.png b/articles/MultiEWCE_files/figure-html/display-1.png
index 85ce86a..98fc255 100644
Binary files a/articles/MultiEWCE_files/figure-html/display-1.png and b/articles/MultiEWCE_files/figure-html/display-1.png differ
diff --git a/articles/docker.html b/articles/docker.html
index 672ad41..6d635ed 100644
--- a/articles/docker.html
+++ b/articles/docker.html
@@ -89,7 +89,7 @@ 

             
             

 

-Vignette updated: Nov-09-2023

+Vignette updated: Nov-14-2023

 

       
       Source: vignettes/docker.Rmd
@@ -165,7 +165,7 @@ 
Session Info
 utils::sessionInfo()

-
## R Under development (unstable) (2023-11-02 r85465)
+
## R Under development (unstable) (2023-11-08 r85496)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.3 LTS
 ## 
@@ -220,7 +220,7 @@ 
Session Info##  [53] ragg_1.2.6                    Rcpp_1.0.11                  
 ##  [55] glue_1.6.2                    SparseArray_1.3.1            
 ##  [57] xfun_0.41                     MatrixGenerics_1.15.0        
-##  [59] GenomeInfoDb_1.39.0           RNOmni_1.0.1.2               
+##  [59] GenomeInfoDb_1.39.1           RNOmni_1.0.1.2               
 ##  [61] dplyr_1.1.3                   BiocManager_1.30.22          
 ##  [63] fastmap_1.1.1                 fansi_1.0.5                  
 ##  [65] caTools_1.18.2                digest_0.6.33                
@@ -255,11 +255,11 @@ 
Session Info## [123] grr_0.9.5                     ggsignif_0.6.4               
 ## [125] gprofiler2_0.2.2              EWCE_1.11.2                  
 ## [127] plyr_1.8.9                    fs_1.6.3                     
-## [129] stringi_1.7.12                viridisLite_0.4.2            
+## [129] stringi_1.8.1                 viridisLite_0.4.2            
 ## [131] ewceData_1.11.0               network_1.18.1               
 ## [133] babelgene_22.9                munsell_0.5.0                
 ## [135] Biostrings_2.71.1             lazyeval_0.2.2               
-## [137] homologene_1.4.68.19.3.27     Matrix_1.6-1.1               
+## [137] homologene_1.4.68.19.3.27     Matrix_1.6-2                 
 ## [139] ExperimentHub_2.11.0          patchwork_1.1.3              
 ## [141] bit64_4.0.5                   ggplot2_3.4.4                
 ## [143] KEGGREST_1.43.0               statmod_1.5.0                
diff --git a/index.html b/index.html
index 0e5c815..dafc09d 100644
--- a/index.html
+++ b/index.html
@@ -95,7 +95,7 @@
 
 

 

-README updated: Nov-09-2023
+README updated: Nov-14-2023
 
 

 
diff --git a/pkgdown.yml b/pkgdown.yml
index a6c764c..b1ca5e2 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   MultiEWCE: MultiEWCE.html
   docker: docker.html
-last_built: 2023-11-09T13:13Z
+last_built: 2023-11-14T17:01Z
 
diff --git a/reference/correlation_heatmap.html b/reference/correlation_heatmap.html
index 56e119d..43d18ed 100644
--- a/reference/correlation_heatmap.html
+++ b/reference/correlation_heatmap.html
@@ -182,7 +182,7 @@ 
Examples

 #> + Version: v2023-10-09
 #> Gathering data from GenCC.
 #> Importing cached file.
-#> + Version: 2023-11-09
+#> + Version: 2023-11-14
 #> Computing all parwise correlations.
 #> Aggregating results by group_var='hpo_name'/'hpo_id'/'ancestor_name'/'ontLvl'/'onset_top'
 #> Loading required namespace: ComplexHeatmap
diff --git a/reference/ewce_para.html b/reference/ewce_para.html
index 7e7c45e..03a773b 100644
--- a/reference/ewce_para.html
+++ b/reference/ewce_para.html
@@ -82,7 +82,8 @@ 
EWCE parallel

   save_dir_tmp = tempdir(),
   parallel_boot = FALSE,
   cores = 1,
-  verbose = FALSE
+  verbose = FALSE,
+  ...
 )

     
 
@@ -165,6 +166,96 @@ 
Arguments

 
verbose

 
Print messages.

 
+
+
...

+
Arguments passed on to EWCE::bootstrap_enrichment_test
sct_data

+
List generated using generate_celltype_data.

+
+    
hits

+
List of gene symbols containing the target gene list.
+Will automatically be converted to human gene symbols
+if geneSizeControl=TRUE.

+
+    
sctSpecies_origin

+
Species that the sct_data 
+originally came from, regardless of its current gene format 
+(e.g. it was previously converted from mouse to human gene orthologs).
+ This is used for computing an appropriate backgrund.

+
+    
output_species

+
Species to convert sct_data and hits to
+(Default: "human").
+See list_species for all available species.

+
+    
method

+
R package to use for gene mapping:
  • "gprofiler" : Slower but more species and genes.
    • 
+
  • "homologene" : Faster but fewer species and genes.
    • 
+
  • "babelgene" : Faster but fewer species and genes.
+Also gives consensus scores for each gene mapping based on a
+ several different data sources.
    • 
+

+
+    
no_cores

+
Number of cores to parallelise
+bootstrapping reps over.

+
+    
geneSizeControl

+
Whether you want to control for
+GC content and transcript length. Recommended if the gene list originates
+from genetic studies (Default: FALSE).
+If set to TRUE, then hits must be from humans.

+
+    
controlledCT

+
[Optional] If not NULL, and instead is the name of a
+cell type, then the bootstrapping controls for expression within that
+cell type.

+
+    
mtc_method

+
Multiple-testing correction method
+(passed to p.adjust).

+
+    
sort_results

+
Sort enrichment results from
+smallest to largest p-values.

+
+    
standardise_sct_data

+
Should sct_data be standardised? 
+if TRUE:
  • When sctSpecies!=output_species
+ the sct_data will be checked for object formatting and 
+ the genes will be converted to the orthologs of the output_species 
+ with standardise_ctd
+  (which calls map_genes internally).
    • 
+
  • When sctSpecies==output_species,
+ the sct_data will be checked for object formatting 
+ with  standardise_ctd, but the gene names 
+ will remain untouched.
    • 
+

+
+    
standardise_hits

+
Should hits be standardised? 
+If TRUE:
  • When genelistSpecies!=output_species, 
+ the genes will be converted to the orthologs of the output_species
+ with convert_orthologs.
    • 
+
  • When genelistSpecies==output_species, 
+ the genes will be standardised with map_genes.
    • 
+
If FALSE, hits will be passed on to subsequent steps as-is.

+
+    
localHub

+
If working offline, add argument localHub=TRUE to work 
+with a local, non-updated hub; It will only have resources available that
+have previously been downloaded. If offline, Please also see BiocManager
+vignette section on offline use to ensure proper functionality.

+
+    
store_gene_data

+
Store sampled gene data for every bootstrap iteration.
+When the number of bootstrap reps is very high (>=100k) and/or
+ the number of genes in hits is very high, you may want
+ to set store_gene_data=FALSE to avoid using excessive amounts of 
+ CPU memory.

+
+  
+

+
 
     

     
Value

@@ -187,7 +278,7 @@ 
Examples

                        list_names = list_names,
                        reps = 10)
 #> Useing cached bg.
-#> + Version: 2023-11-09
+#> + Version: 2023-11-14
 #> Computing gene counts.
 

     
diff --git a/reference/ewce_plot.html b/reference/ewce_plot.html
index 17fece6..5c57405 100644
--- a/reference/ewce_plot.html
+++ b/reference/ewce_plot.html
@@ -130,7 +130,7 @@ 
Examples

 #> loading from cache
 #> see ?ewceData and browseVignettes('ewceData') for documentation
 #> loading from cache
-#> 1 core(s) assigned as workers (3 reserved).
+#> 1 core(s) assigned as workers (1 reserved).
 #> Generating gene background for mouse x human ==> human
 #> Gathering ortholog reports.
 #> Retrieving all genes using: homologene.
diff --git a/reference/frequency_barplot.html b/reference/frequency_barplot.html
index 02782f0..b7f6bcd 100644
--- a/reference/frequency_barplot.html
+++ b/reference/frequency_barplot.html
@@ -69,7 +69,7 @@ 
Gene and phenotype frequencies bar plot

     
frequency_barplot(
   results = load_example_results(),
   phenotype_to_genes = load_phenotype_to_genes(),
-  show_plot = TRUE,
+  show_plot = FALSE,
   verbose = TRUE
 )

     
@@ -122,7 +122,6 @@ 
Examples

 #> ℹ All local files already up-to-date!
 #> 96.2% of rows are NA.
 #> 99.3% of rows are NA.
-
 

     
   
diff --git a/reference/frequency_histogram.html b/reference/frequency_histogram.html
index 105e89a..04d9dec 100644
--- a/reference/frequency_histogram.html
+++ b/reference/frequency_histogram.html
@@ -69,7 +69,7 @@ 
Gene and phenotype frequencies histogram

     
frequency_histogram(
   results = load_example_results(),
   phenotype_to_genes = load_phenotype_to_genes(),
-  show_plot = TRUE,
+  show_plot = FALSE,
   verbose = TRUE
 )

     
@@ -121,8 +121,6 @@ 
Examples

 #> Adding level-3 ancestor to each HPO ID.
 #> ℹ All local files already up-to-date!
 #> Warning: Ignoring unknown parameters: `binwidth`, `bins`, and `pad`
-#> Warning: Removed 14889 rows containing non-finite values (`stat_density()`).
-
diff --git a/reference/gen_overlap.html b/reference/gen_overlap.html index 233882d..7570642 100644 --- a/reference/gen_overlap.html +++ b/reference/gen_overlap.html @@ -176,9 +176,9 @@

Examples

#> The following object is masked from ‘package:base’: #> #> %||% -#> 1.08120226860046 +#> 2.21393299102783 #> -#> Saving results ==> /tmp/RtmpiGoWD4/gen_overlap.rds +#> Saving results ==> /tmp/Rtmp0tNWxK/gen_overlap.rds diff --git a/reference/gen_results.html b/reference/gen_results.html index 72afe60..2296333 100644 --- a/reference/gen_results.html +++ b/reference/gen_results.html @@ -93,7 +93,8 @@

Generate results

parallel_boot = FALSE, save_dir_tmp = NULL, save_dir = tempdir(), - verbose = 1 + verbose = 1, + ... ) @@ -180,6 +181,96 @@

Arguments

verbose

Print messages.

+ +
...
+

Arguments passed on to EWCE::bootstrap_enrichment_test

sct_data
+

List generated using generate_celltype_data.

+ +
hits
+

List of gene symbols containing the target gene list. +Will automatically be converted to human gene symbols +if geneSizeControl=TRUE.

+ +
sctSpecies_origin
+

Species that the sct_data +originally came from, regardless of its current gene format +(e.g. it was previously converted from mouse to human gene orthologs). + This is used for computing an appropriate backgrund.

+ +
output_species
+

Species to convert sct_data and hits to +(Default: "human"). +See list_species for all available species.

+ +
method
+

R package to use for gene mapping:

  • "gprofiler" : Slower but more species and genes.

    • +

  • "homologene" : Faster but fewer species and genes.

    • +

  • "babelgene" : Faster but fewer species and genes. +Also gives consensus scores for each gene mapping based on a + several different data sources.

    • +
+ +
no_cores
+

Number of cores to parallelise +bootstrapping reps over.

+ +
geneSizeControl
+

Whether you want to control for +GC content and transcript length. Recommended if the gene list originates +from genetic studies (Default: FALSE). +If set to TRUE, then hits must be from humans.

+ +
controlledCT
+

[Optional] If not NULL, and instead is the name of a +cell type, then the bootstrapping controls for expression within that +cell type.

+ +
mtc_method
+

Multiple-testing correction method +(passed to p.adjust).

+ +
sort_results
+

Sort enrichment results from +smallest to largest p-values.

+ +
standardise_sct_data
+

Should sct_data be standardised? +if TRUE:

  • When sctSpecies!=output_species + the sct_data will be checked for object formatting and + the genes will be converted to the orthologs of the output_species + with standardise_ctd + (which calls map_genes internally).

    • +

  • When sctSpecies==output_species, + the sct_data will be checked for object formatting + with standardise_ctd, but the gene names + will remain untouched.

    • +
+ +
standardise_hits
+

Should hits be standardised? +If TRUE:

  • When genelistSpecies!=output_species, + the genes will be converted to the orthologs of the output_species + with convert_orthologs.

    • +

  • When genelistSpecies==output_species, + the genes will be standardised with map_genes.

    • +

If FALSE, hits will be passed on to subsequent steps as-is.

+ +
localHub
+

If working offline, add argument localHub=TRUE to work +with a local, non-updated hub; It will only have resources available that +have previously been downloaded. If offline, Please also see BiocManager +vignette section on offline use to ensure proper functionality.

+ +
store_gene_data
+

Store sampled gene data for every bootstrap iteration. +When the number of bootstrap reps is very high (>=100k) and/or + the number of genes in hits is very high, you may want + to set store_gene_data=FALSE to avoid using excessive amounts of + CPU memory.

+ + +
+

Value

@@ -209,13 +300,13 @@

Examples

#> Validating gene lists.. #> 2 / 5 gene lists are valid. #> Useing cached bg. -#> + Version: 2023-11-09 +#> + Version: 2023-11-14 #> Background contains 62,663 genes. #> Computing gene counts. #> Computing gene counts. -#> Done in: 3.7 seconds. +#> Done in: 5.5 seconds. #> -#> Saving results ==> /tmp/RtmpiGoWD4/gen_results.rds +#> Saving results ==> /tmp/Rtmp0tNWxK/gen_results.rds
diff --git a/reference/get_bg.html b/reference/get_bg.html index b9a93cb..c6397b1 100644 --- a/reference/get_bg.html +++ b/reference/get_bg.html @@ -182,7 +182,7 @@

Value

Examples

bg <- get_bg()
 #> Useing cached bg.
-#> + Version: 2023-11-09
+#> + Version: 2023-11-14
diff --git a/reference/get_unfinished_list_names.html b/reference/get_unfinished_list_names.html index 4d9a109..5436011 100644 --- a/reference/get_unfinished_list_names.html +++ b/reference/get_unfinished_list_names.html @@ -109,7 +109,7 @@

Examples

reps = 10, save_dir_tmp = save_dir_tmp) #> Useing cached bg. -#> + Version: 2023-11-09 +#> + Version: 2023-11-14 #> Computing gene counts. unfinished <- get_unfinished_list_names(list_names = gene_data$hpo_id, save_dir_tmp = save_dir_tmp) diff --git a/reference/merge_results.html b/reference/merge_results.html index 25b0c4d..2b103b9 100644 --- a/reference/merge_results.html +++ b/reference/merge_results.html @@ -120,7 +120,7 @@

Examples

#> Gene table with 62,663 rows retrieved. #> Returning all 62,663 genes from human. #> Returning 62,663 unique genes from entire human genome. -#> + Version: 2023-11-09 +#> + Version: 2023-11-14 #> Computing gene counts. all_results <- merge_results(res_files=res_files) diff --git a/reference/prioritise_targets.html b/reference/prioritise_targets.html index 9dc3e8b..0f6cc40 100644 --- a/reference/prioritise_targets.html +++ b/reference/prioritise_targets.html @@ -564,7 +564,7 @@

Examples

#> Annotating gene-disease associations with Evidence score #> Gathering data from GenCC. #> Importing cached file. -#> + Version: 2023-11-09 +#> + Version: 2023-11-14 #> Prioritised targets: step='keep_evidence' #> - Rows: 2 #> - Phenotypes: 1 diff --git a/reference/prioritise_targets_network.html b/reference/prioritise_targets_network.html index 6f6517a..13f7014 100644 --- a/reference/prioritise_targets_network.html +++ b/reference/prioritise_targets_network.html @@ -253,7 +253,7 @@

Examples

#> Loading required namespace: tidygraph #> Creating network. #> Creating plot. -#> Saving plot ==> /tmp/RtmpiGoWD4/file180c156de1e3_prioritise_targets_network.html +#> Saving plot ==> /tmp/Rtmp0tNWxK/file26a91e080e96_prioritise_targets_network.html diff --git a/reference/report_plot.html b/reference/report_plot.html index 351eccf..1cd7662 100644 --- a/reference/report_plot.html +++ b/reference/report_plot.html @@ -184,7 +184,7 @@

Examples

#> ℹ The deprecated feature was likely used in the MultiEWCE package. #> Please report the issue at #> <https://github.com/neurogenomics/MultiEWCE/issues>. -#> Saving plot ==> /tmp/RtmpiGoWD4/file180c201fc7e6_report_plot.pdf +#> Saving plot ==> /tmp/Rtmp0tNWxK/file26a92ff8c571_report_plot.pdf #> Saving 6.67 x 6.67 in image