|
38
|
1 require("data.table", quietly = TRUE)
|
|
|
2 require("GEOquery", quietly = TRUE)
|
|
|
3
|
|
|
4
|
|
|
5 options(warn = -1)
|
|
|
6 options("download.file.method"="wget")
|
|
|
7 args <- commandArgs(trailingOnly = TRUE)
|
|
|
8 GSMTable = args[1]
|
|
|
9 MetaTable = args[2]
|
|
|
10
|
|
|
11 TAB = fread(GSMTable)
|
|
|
12
|
|
|
13
|
|
|
14 if (is.null(TAB)) {
|
|
|
15 stop("Must specify input files")
|
|
|
16 } else {
|
|
|
17 options(download.file.method.GEOquery = "wget")
|
|
|
18
|
|
|
19
|
|
|
20 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
|
|
|
21 MetaData <- data.frame(Meta(GEODataTable))
|
|
|
22
|
|
|
23 write.table(MetaData, MetaTable, row.names = FALSE, sep = "\t")
|
|
|
24 }
|
|
|
25
|
