Mercurial > repos > testtool > get_gsm

comparison getGSMdata/.Rhistory @ 8:5e1d49abfc99 draft

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author testtool
date Mon, 06 Feb 2017 05:17:56 -0500
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children c1bf6f112a19
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7:3eb1073638d7 8:5e1d49abfc99
1 GSMTable <- ("test-data/GSMTable.txt")
2 write.table(samples, GSMTable, row.names = FALSE, sep = "\t")
3 ?write.table
4 GSE <- "GSE51547"
5 search1 <- entrez_search(db = "gds", term = GSE, retmax = 1)
6 require("rentrez", quietly = TRUE)
7 search1 <- entrez_search(db = "gds", term = GSE, retmax = 1)
8 rec2 <- entrez_summary(db = "gds",
9 id = search1$ids,
10 version = "2.0")
11 extract <- extract_from_esummary(rec2,rownames(summary(rec2)))
12 samples <- extract$samples
13 colnames(samples)[which(names(samples) == "accession")] <- "ID"
14 colnames(samples)[which(names(samples) == "title")] <- "Phenotype"
15 write.table(samples, GSMTable, row.names = FALSE, sep = "\t",quote = FALSE)
16 write.table(samples, file=GSMTable.txt, row.names = FALSE, sep = "\t",quote = FALSE)
17 write.table(samples, file="GSMTable.txt", row.names = FALSE, sep = "\t",quote = FALSE)