changeset 35:31fe37b30836 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/test-data/getGSMdata.R	Mon Jul 31 12:37:58 2017 -0400
@@ -0,0 +1,26 @@
+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"
+
+samples$Phenotype<-gsub("\\s", "",samples$Phenotype) 
+
+write.table(samples, GSMTable, row.names = FALSE,quote=FALSE,sep="\t")
+
+