Mercurial > repos > sblanck > mpagenomics
view selectionExtracted.R @ 2:b0346f5e9e45 draft
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 7679c75b4a95df45311603e2dceda55b159ffb4b-dirty
author | sblanck |
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date | Fri, 29 May 2020 10:48:28 -0400 |
parents | 4d539083cf7f |
children | 3fcbb8030fcc |
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#!/usr/bin/env Rscript # setup R error handling to go to stderr options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) # we need that to not crash galaxy with an UTF8 error on German LC settings. loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") library("optparse") ##### Read options option_list=list( make_option("--input",type="character",default=NULL, dest="input"), make_option("--output",type="character",default=NULL, dest="output"), make_option("--new_file_path",type="character",default=NULL, dest="new_file_path"), make_option("--response",type="character",default=NULL, dest="response"), make_option("--loss",type="character",default=NULL, dest="loss"), make_option("--folds",type="character",default=NULL, dest="folds"), make_option("--outputlog",type="character",default=NULL, dest="outputlog"), make_option("--log",type="character",default=NULL, dest="log") ); opt_parser = OptionParser(option_list=option_list); opt = parse_args(opt_parser); if(is.null(opt$input)){ print_help(opt_parser) stop("input required.", call.=FALSE) } #loading libraries input=opt$input response=opt$response output=opt$output tmp_dir=opt$new_file_path nbFolds=as.numeric(opt$folds) loss=opt$loss log=opt$log outputlog=opt$outputlog #args<-commandArgs(TRUE) # #input=args[1] #response=args[2] #tmp_dir=args[3] #nbFolds=as.numeric(args[4]) #loss=args[5] #output=args[6] library(MPAgenomics) workdir=file.path(tmp_dir, "mpagenomics") setwd(workdir) if (outputlog){ sinklog <- file(log, open = "wt") sink(sinklog ,type = "output") sink(sinklog, type = "message") } CN=read.table(input,header=TRUE,check.names=FALSE) drops=c("chromosome","position","probeName") CNsignal=CN[,!(names(CN)%in% drops)] samples=names(CNsignal) CNsignalMatrix=t(data.matrix(CNsignal)) resp=read.table(response,header=TRUE,sep=",") listOfFile=resp[[1]] responseValue=resp[[2]] index = match(listOfFile,rownames(CNsignalMatrix)) responseValueOrder=responseValue[index] result=variableSelection(CNsignalMatrix,responseValueOrder,nbFolds=nbFolds,loss=loss,plot=TRUE) CNsignalResult=CN[result$markers.index,(names(CN)%in% drops)] CNsignalResult["coefficient"]=result$coefficient CNsignalResult["index"]=result$markers.index if (outputlog){ sink(type="output") sink(type="message") close(sinklog) } #sink(output) #print(format(CNsignalResult),row.names=FALSE) #sink() write.table(CNsignalResult,output,row.names = FALSE, quote=FALSE, sep = "\t")