Mercurial > repos > testtool > get_gsm
diff getGSMdata/getGSMdata.R @ 26:ac5415190777 draft
Uploaded
author | testtool |
---|---|
date | Wed, 15 Feb 2017 10:21:18 -0500 |
parents | 5e1d49abfc99 |
children | 0051ff360c64 |
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--- a/getGSMdata/getGSMdata.R Mon Feb 06 10:31:24 2017 -0500 +++ b/getGSMdata/getGSMdata.R Wed Feb 15 10:21:18 2017 -0500 @@ -1,9 +1,12 @@ require("rentrez", quietly = TRUE) args <- commandArgs(trailingOnly = TRUE) + GSE = args[1] GSMTable = args[2] + + search1 <- entrez_search(db = "gds", term = GSE, retmax = 1) rec2 <- entrez_summary(db = "gds", @@ -16,5 +19,8 @@ colnames(samples)[which(names(samples) == "accession")] <- "ID" colnames(samples)[which(names(samples) == "title")] <- "Phenotype" -write.table(samples, GSMTable, row.names = FALSE, sep = "\t",quote = FALSE) +samples$Phenotype<-gsub("\\s", "",samples$Phenotype) +write.table(samples, GSMTable, row.names = FALSE,quote=FALSE,sep="\t") + +