comparison GEOQuery.R @ 4:2c9e44ff68dc draft

use optparse

3:b01c4f260085

library(GEOquery)


cargs<-commandArgs()
cargs<-cargs[(which(cargs=="--args")+1):length(cargs)]

GEOQueryID<-cargs[[1]]
GEOQueryData<-cargs[[2]]
GEOQueryRData<-cargs[[3]]
conditionFile<-cargs[[4]]
transformation<-cargs[[5]]

data1 = getGEO(GEOQueryID)
eset=data1[[1]]

#check if datas are in log2 space
normalization<-function(data){
	ex <- exprs(data)

4:2c9e44ff68dc

#!/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("--id",type="character",default=NULL,help="GSE ID from GEO databse (required)"),
		make_option("--transformation",type="character",default=NULL,help="log2 transformation (required)"),
		make_option("--data",type="character",default=NULL,help="A table containing the expression data"),
		make_option("--rdata",type="character",default="NULL",help="rdata object containing eset object"),
		make_option("--conditions",type="character",default=NULL,help="Text file summarizing conditions of the experiment")
		
);

opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);

if(is.null(opt$id)){
	print_help(opt_parser)
	stop("GEOdata id required.", call.=FALSE)
}

#loading libraries
suppressPackageStartupMessages(require(GEOquery))

GEOQueryID=opt$id
GEOQueryData=opt$data
GEOQueryRData=opt$rdata
conditionFile=opt$conditions
transformation=opt$transformation

data1=getGEO(GEOQueryID)
eset=data1[[1]]

#check if datas are in log2 space
normalization<-function(data){
	ex <- exprs(data)