Mercurial > repos > testtool > get_gr_set

annotate GRsetFromGEO/GRsetFromGEO.R @ 52:d6c7c3ed3290 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author testtool
date Thu, 10 Aug 2017 06:19:36 -0400
parents fe7d4d8591c5
children 5752f23e451f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
39
05f6acc80f47 Uploaded
testtool
parents: 38
diff changeset
1 require(minfi, quietly = TRUE)
05f6acc80f47 Uploaded
testtool
parents: 38
diff changeset
2 require(IlluminaHumanMethylation450kanno.ilmn12.hg19, quietly = TRUE)
05f6acc80f47 Uploaded
testtool
parents: 38
diff changeset
3
5
7511130b5068 Uploaded
testtool
parents:
diff changeset
4 options(warn = -1)
22
71a8c9b37d45 Uploaded
testtool
parents: 21
diff changeset
5 options('download.file.method.GEOquery' = 'wget')
21
07f0fc6e4d1d Uploaded
testtool
parents: 17
diff changeset
6 options('GEOquery.inmemory.gpl'=FALSE)
17
3431c6054674 Uploaded
testtool
parents: 16
diff changeset
7
5
7511130b5068 Uploaded
testtool
parents:
diff changeset
8
7511130b5068 Uploaded
testtool
parents:
diff changeset
9 args <- commandArgs(trailingOnly = TRUE)
16
ceaf71c74547 Uploaded
testtool
parents: 14
diff changeset
10 input = args[1]
5
7511130b5068 Uploaded
testtool
parents:
diff changeset
11 output = args[2]
39
05f6acc80f47 Uploaded
testtool
parents: 38
diff changeset
12
42
fe7d4d8591c5 Uploaded
testtool
parents: 39
diff changeset
13 GRset <- minfi::getGenomicRatioSetFromGEO(input)
5
7511130b5068 Uploaded
testtool
parents:
diff changeset
14
7511130b5068 Uploaded
testtool
parents:
diff changeset
15 save(GRset,file = output)
38
88d2c717105e Uploaded
testtool
parents: 33
diff changeset
16
42
fe7d4d8591c5 Uploaded
testtool
parents: 39
diff changeset
17 ??getGenomicRatioSetFromGEO