Mercurial > repos > testtool > get_gr_set

annotate GRsetFromGEO/GRsetFromGEO.R @ 31:b61aac190ca6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author testtool
date Mon, 10 Jul 2017 10:51:46 -0400
parents 71a8c9b37d45
children 296124126b94
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
c3b28b232e64 Uploaded
testtool
parents: 13
diff changeset
1 require("minfi", quietly = TRUE)
c3b28b232e64 Uploaded
testtool
parents: 13
diff changeset
2
5
7511130b5068 Uploaded
testtool
parents:
diff changeset
3 options(warn = -1)
22
71a8c9b37d45 Uploaded
testtool
parents: 21
diff changeset
4 options('download.file.method.GEOquery' = 'wget')
21
07f0fc6e4d1d Uploaded
testtool
parents: 17
diff changeset
5 options('GEOquery.inmemory.gpl'=FALSE)
17
3431c6054674 Uploaded
testtool
parents: 16
diff changeset
6
5
7511130b5068 Uploaded
testtool
parents:
diff changeset
7
7511130b5068 Uploaded
testtool
parents:
diff changeset
8 args <- commandArgs(trailingOnly = TRUE)
16
ceaf71c74547 Uploaded
testtool
parents: 14
diff changeset
9 input = args[1]
5
7511130b5068 Uploaded
testtool
parents:
diff changeset
10 output = args[2]
7511130b5068 Uploaded
testtool
parents:
diff changeset
11
16
ceaf71c74547 Uploaded
testtool
parents: 14
diff changeset
12 GRset <- getGenomicRatioSetFromGEO(input)
5
7511130b5068 Uploaded
testtool
parents:
diff changeset
13
7511130b5068 Uploaded
testtool
parents:
diff changeset
14 save(GRset,file = output)