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comparison GEOQuery.R @ 0:1024245abc70 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
author sblanck
date Thu, 22 Feb 2018 08:38:22 -0500
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-1:000000000000 0:1024245abc70
1 #!/usr/bin/env Rscript
2 # setup R error handling to go to stderr
3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
4
5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
7
8 library("optparse")
9
10 ##### Read options
11 option_list=list(
12 make_option("--id",type="character",default=NULL,help="GSE ID from GEO databse (required)"),
13 make_option("--transformation",type="character",default=NULL,help="log2 transformation (required)"),
14 make_option("--data",type="character",default=NULL,help="A table containing the expression data"),
15 make_option("--rdata",type="character",default="NULL",help="rdata object containing eset object"),
16 make_option("--conditions",type="character",default=NULL,help="Text file summarizing conditions of the experiment")
17
18 );
19
20 opt_parser = OptionParser(option_list=option_list);
21 opt = parse_args(opt_parser);
22
23 if(is.null(opt$id)){
24 print_help(opt_parser)
25 stop("GEOdata id required.", call.=FALSE)
26 }
27
28 #loading libraries
29 suppressPackageStartupMessages(require(GEOquery))
30
31 GEOQueryID=opt$id
32 GEOQueryData=opt$data
33 GEOQueryRData=opt$rdata
34 conditionFile=opt$conditions
35 transformation=opt$transformation
36
37 data1=getGEO(GEOQueryID)
38 eset=data1[[1]]
39
40 #check if datas are in log2 space
41 normalization<-function(data){
42 ex <- exprs(data)
43 qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
44 LogC <- (qx[5] > 100) ||
45 (qx[6]-qx[1] > 50 && qx[2] > 0) ||
46 (qx[2] > 0 && qx[2] < 1 && qx[4] > 1 && qx[4] < 2)
47 if (LogC) { ex[which(ex <= 0)] <- NaN
48 return (log2(ex)) } else {
49 return (ex)
50 }
51 }
52
53 if (transformation=="auto"){
54 exprs(eset)=normalization(eset)
55 } else if (transformation=="yes"){
56 exprs(eset)=log2(exprs(eset))
57 }
58
59 matrixData=exprs(eset)
60 write.table(matrixData,col.names=NA,row.names=TRUE,sep="\t",file=GEOQueryData)
61
62 #Construcion of condition file
63 #if there is data in "source_name_ch1" field, we keep this data as a condition
64 #else we keep the "description" field data.
65 if (length(unique(tolower(pData(data1[[1]])["source_name_ch1"][,1])))>1)
66 {
67 conditions=pData(data1[[1]])["source_name_ch1"]
68 description=paste0(as.vector(pData(data1[[1]])["geo_accession"][,1]), " ",as.vector(pData(data1[[1]])["title"][,1]), " ", as.vector(conditions[,1]))
69 } else
70 {
71 conditions=pData(data1[[1]])["description"]
72 description=paste0(as.vector(pData(data1[[1]])["geo_accession"][,1]), " ",as.vector(pData(data1[[1]])["title"][,1]), " ", as.vector(conditions[,1]))
73 }
74
75 conditions[,1]=tolower(conditions[,1])
76 pData(eset)["source_name_ch1"]=conditions
77
78 write.table(cbind(conditions,description),quote = FALSE,col.names = FALSE, row.names=TRUE,file=conditionFile,sep="\t")
79 save(eset,conditions,file=GEOQueryRData)