optionally keep genes in enrichr

uzh · Dec 13, 2024 · 8109a78 · 8109a78
1 parent 81a203b
commit 8109a78
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Showing 2 changed files with 7 additions and 8 deletions.
diff --git a/R/app-ScSeurat.R b/R/app-ScSeurat.R
@@ -408,8 +408,13 @@ addCellQcToSeurat <- function(scData, param=NULL, BPPARAM=NULL, ribosomalGenes=N
   return(scData)
 }
 
-querySignificantClusterAnnotationEnrichR <- function(genesPerCluster, dbs, overlapGeneCutOff = 3, adjPvalueCutOff = 0.001, reportTopN = 5) {
+querySignificantClusterAnnotationEnrichR <- function(genesPerCluster, dbs, overlapGeneCutOff = 3, adjPvalueCutOff = 0.001, 
+                                                     reportTopN = 5, keepGenes=FALSE) {
   enrichRout <- list()
+  columnsToKeep <- c("Term", "Cluster", "Overlap", "OverlapGenesN", "Adjusted.P.value", "Odds.Ratio", "Combined.Score")
+  if (keepGenes){
+    columnsToKeep <- c(columnsToKeep, "Genes")
+  }
   for (cluster in unique(names(genesPerCluster))) {
     enriched <- enrichr(as.character(genesPerCluster[[cluster]]), dbs)
 
@@ -422,7 +427,7 @@ querySignificantClusterAnnotationEnrichR <- function(genesPerCluster, dbs, overl
           filter(., Adjusted.P.value < adjPvalueCutOff) %>%
           filter(., OverlapGenesN > overlapGeneCutOff) %>%
           head(reportTopN)
-        enrichRout[[cluster]][[db]] <- enriched_db[, c("Term", "Cluster", "Overlap", "OverlapGenesN", "Adjusted.P.value", "Odds.Ratio", "Combined.Score")]
+        enrichRout[[cluster]][[db]] <- enriched_db[, columnsToKeep]
       }
     }
   }

diff --git a/inst/extdata/EZ_GLOBAL_VARIABLES.txt b/inst/extdata/EZ_GLOBAL_VARIABLES.txt
@@ -62,12 +62,6 @@ CNVNATOR="/usr/local/ngseq/src/CNVnator_v0.3.3/src/cnvnator"
 ## SMRT 
 SMRT_CMD="SMRT=/misc/ngseq8/opt/smrtanalysis.2.3.0/install/smrtanalysis_2.3.0.140936; source $SMRT/etc/setup.sh; fofnToSmrtpipeInput.py input.fofn > input.xml; smrtpipe.py --params=settings.xml xml:input.xml"
 
-############# R-SGE options
-# RSGE_RUN_JOB="/usr/local/ngseq/opt/sushi_scripts/Rsge/RunSgeJob"
-# RSGE_MONITOR_JOB="/usr/local/ngseq/opt/sushi_scripts/Rsge/MonitorJob.sh"
-# QSUB="/usr/local/ge62/bin/lx24-amd64/qsub"
-# SGE_ROOT="/usr/local/ge62"
-
 
 ## METAGENONMICS (MOTHUR-UPARSE-QIIME)
 METAGENOMICS_ROOT="/usr/local/ngseq/templateFiles/"