view getGSMdata/.Rhistory @ 38:af9cb4b9f01e draft default tip

Uploaded

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)
??entrez_summary
??getGEO
??bumphunter
??annotatePeak