diff selectionExtracted.R @ 4:3fcbb8030fcc draft

"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
author sblanck
date Mon, 12 Apr 2021 14:47:09 +0000
parents 4d539083cf7f
children
line wrap: on
line diff
--- a/selectionExtracted.R	Tue Jun 16 04:34:09 2020 -0400
+++ b/selectionExtracted.R	Mon Apr 12 14:47:09 2021 +0000
@@ -50,7 +50,9 @@
 #output=args[6]
 
 library(MPAgenomics)
-workdir=file.path(tmp_dir, "mpagenomics")
+workdir=file.path(tmp_dir)
+if (!dir.exists(workdir))
+  dir.create(workdir, showWarnings = TRUE, recursive = TRUE)
 setwd(workdir)
 
 if (outputlog){
@@ -70,7 +72,7 @@
 index = match(listOfFile,rownames(CNsignalMatrix))
 responseValueOrder=responseValue[index]
 
-result=variableSelection(CNsignalMatrix,responseValueOrder,nbFolds=nbFolds,loss=loss,plot=TRUE)
+result=variableSelection(CNsignalMatrix,responseValueOrder,nbFolds=nbFolds,loss=loss,plot=FALSE)
 
 CNsignalResult=CN[result$markers.index,(names(CN)%in% drops)]