Mercurial > repos > testtool > get_gsm

view getGSMdata/getGSMdata.R @ 12:ae5c9af80d3c draft

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author testtool
date Mon, 06 Feb 2017 06:38:55 -0500
parents 5e1d49abfc99
children ac5415190777
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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",
                       id = search1$ids,
                       version = "2.0")

extract <- extract_from_esummary(rec2,rownames(summary(rec2)))

samples <- extract$samples
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)