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author testtool
date Mon, 06 Feb 2017 09:07:58 -0500
parents 5e1d49abfc99
children c1bf6f112a19
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GSMTable <- ("test-data/GSMTable.txt")
write.table(samples, GSMTable, row.names = FALSE, sep = "\t")
?write.table
GSE <- "GSE51547"
search1 <- entrez_search(db = "gds", term = GSE, retmax = 1)
require("rentrez", quietly = TRUE)
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)
write.table(samples, file=GSMTable.txt, row.names = FALSE, sep = "\t",quote = FALSE)
write.table(samples, file="GSMTable.txt", row.names = FALSE, sep = "\t",quote = FALSE)