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comparison GEO/getGEO.R @ 1:7230be4d8c66 draft

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author testtool
date Thu, 09 Feb 2017 12:26:33 -0500
parents 4fb1765f3979
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0:4fb1765f3979 1:7230be4d8c66
2 require("data.table", quietly = TRUE) 2 require("data.table", quietly = TRUE)
3 require("GEOquery", quietly = TRUE) 3 require("GEOquery", quietly = TRUE)
4 require("rtracklayer", quietly = TRUE) 4 require("rtracklayer", quietly = TRUE)
5 require("FDb.InfiniumMethylation.hg19", quietly = TRUE) 5 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
6 6
7 options("download.file.method"="wget") 7 options("download.file.method.GEOquery"="wget")
8 options(warn = -1) 8 options(warn = -1)
9 9
10 args <- commandArgs(trailingOnly = TRUE) 10 args <- commandArgs(trailingOnly = TRUE)
11 GSMTable = args[1] 11 GSMTable = args[1]
12 MetaTable = args[2] 12 MetaTable = args[2]