Mercurial > repos > testtool > get_gr_set

comparison GRsetFromGEO/GRsetFromGEO.R @ 38:88d2c717105e draft

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author testtool
date Mon, 24 Jul 2017 10:39:43 -0400
parents ae82fab7c544
children 05f6acc80f47
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37:10996f6ddcb5 38:88d2c717105e
1 require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)
2 require("minfi", quietly = TRUE)
3
4 options(warn = -1) 1 options(warn = -1)
5 options('download.file.method.GEOquery' = 'wget') 2 options('download.file.method.GEOquery' = 'wget')
6 options('GEOquery.inmemory.gpl'=FALSE) 3 options('GEOquery.inmemory.gpl'=FALSE)
7 4
8 5
9 args <- commandArgs(trailingOnly = TRUE) 6 args <- commandArgs(trailingOnly = TRUE)
10 input = args[1] 7 input = args[1]
11 output = args[2] 8 output = args[2]
12 9 input <- 'GSE51547'
13 GRset <- getGenomicRatioSetFromGEO(input) 10 GRset <- getGenomicRatioSetFromGEO(input)
14 11
15 save(GRset,file = output) 12 save(GRset,file = output)
13