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comparison getMETAdata/getMETAdata.R @ 72:cb14dbc2fd60 draft

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author testtool
date Tue, 15 Aug 2017 06:06:55 -0400
parents 81b5c08c21e1
children
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71:81b5c08c21e1 72:cb14dbc2fd60
1 require("data.table", quietly = TRUE)
2 require("GEOquery", quietly = TRUE) 1 require("GEOquery", quietly = TRUE)
3 2
4 3
5 options(warn = -1) 4 options(warn = -1)
6 options("download.file.method"="wget") 5 options("download.file.method"="wget")
7 args <- commandArgs(trailingOnly = TRUE) 6 args <- commandArgs(trailingOnly = TRUE)
8 GSMTable = args[1] 7 GSMTable = args[1]
9 MetaTable = args[2] 8 MetaTable = args[2]
10 9
11 TAB = fread(GSMTable) 10 TAB = read.table(GSMTable)
12 11
13 12
14 if (is.null(TAB)) { 13 if (is.null(TAB)) {
15 stop("Must specify input files") 14 stop("Must specify input files")
16 } else { 15 } else {