Mercurial > repos > sblanck > mpagenomics

comparison selectionExtracted.R @ 4:3fcbb8030fcc draft

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"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
comparison
equal deleted inserted replaced
3:94fc6ed13946 4:3fcbb8030fcc
48 #nbFolds=as.numeric(args[4]) 48 #nbFolds=as.numeric(args[4])
49 #loss=args[5] 49 #loss=args[5]
50 #output=args[6] 50 #output=args[6]
51 51
52 library(MPAgenomics) 52 library(MPAgenomics)
53 workdir=file.path(tmp_dir, "mpagenomics") 53 workdir=file.path(tmp_dir)
54 if (!dir.exists(workdir))
55 dir.create(workdir, showWarnings = TRUE, recursive = TRUE)
54 setwd(workdir) 56 setwd(workdir)
55 57
56 if (outputlog){ 58 if (outputlog){
57 sinklog <- file(log, open = "wt") 59 sinklog <- file(log, open = "wt")
58 sink(sinklog ,type = "output") 60 sink(sinklog ,type = "output")
68 listOfFile=resp[[1]] 70 listOfFile=resp[[1]]
69 responseValue=resp[[2]] 71 responseValue=resp[[2]]
70 index = match(listOfFile,rownames(CNsignalMatrix)) 72 index = match(listOfFile,rownames(CNsignalMatrix))
71 responseValueOrder=responseValue[index] 73 responseValueOrder=responseValue[index]
72 74
73 result=variableSelection(CNsignalMatrix,responseValueOrder,nbFolds=nbFolds,loss=loss,plot=TRUE) 75 result=variableSelection(CNsignalMatrix,responseValueOrder,nbFolds=nbFolds,loss=loss,plot=FALSE)
74 76
75 CNsignalResult=CN[result$markers.index,(names(CN)%in% drops)] 77 CNsignalResult=CN[result$markers.index,(names(CN)%in% drops)]
76 78
77 CNsignalResult["coefficient"]=result$coefficient 79 CNsignalResult["coefficient"]=result$coefficient
78 CNsignalResult["index"]=result$markers.index 80 CNsignalResult["index"]=result$markers.index