| Previous changeset 2:7c896d0c6119 (2017-02-06) Next changeset 4:7b6d8d0b3253 (2017-02-06) |
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Commit message:
Uploaded |
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added:
getGSMdata.R |
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| diff -r 7c896d0c6119 -r c90a3ff42982 getGSMdata.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGSMdata.R Mon Feb 06 05:08:04 2017 -0500 |
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| @@ -0,0 +1,20 @@ +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) + |