Mercurial > repos > proteore > proteore_clusterprofiler

changeset 26:c8bff18c102b draft

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planemo upload commit d884b75cfc292105807c42c58f864d536dc9e431-dirty
author proteore
date Wed, 21 Nov 2018 08:22:13 -0500
parents 3a66e1e65c02
children 54f8e6f5c59d
files GO-enrich.R cluster_profiler.xml
diffstat 2 files changed, 3 insertions(+), 1 deletions(-) [+]
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line diff
--- a/GO-enrich.R	Tue Nov 06 08:56:05 2018 -0500
+++ b/GO-enrich.R	Wed Nov 21 08:22:13 2018 -0500
@@ -264,12 +264,14 @@
   for (onto in ontology) {
     if (args$go_represent == "true") {
       ggo<-repartition.GO(gene, orgdb, onto, level, readable=TRUE)
+      ggo <- as.data.frame(apply(ggo, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" and " " to NA
       output_path = paste("cluster_profiler_GGO_",onto,".tsv",sep="")
       write.table(ggo, output_path, sep="\t", row.names = FALSE, quote = FALSE )
     }
 
     if (args$go_enrich == "true") {
       ego<-enrich.GO(gene, universe_gene, orgdb, onto, pval_cutoff, qval_cutoff,plot)
+      ego <- as.data.frame(apply(ego, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" and " " to NA
       output_path = paste("cluster_profiler_EGO_",onto,".tsv",sep="")
       write.table(ego, output_path, sep="\t", row.names = FALSE, quote = FALSE )
     }
--- a/cluster_profiler.xml	Tue Nov 06 08:56:05 2018 -0500
+++ b/cluster_profiler.xml	Wed Nov 21 08:22:13 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.11.06">
+<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.11.21">
     <description>(Human, Mouse, Rat) (clusterProfiler)</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>