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comparison GRsetFromGEO/GRsetFromGEO.R @ 43:660897ee0d12 draft

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author testtool
date Mon, 24 Apr 2017 10:31:20 -0400
parents 4987433afb56
children 7aeee7c02c4d
comparison
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42:4987433afb56 43:660897ee0d12
1 require("BiocGenerics", quietly = TRUE)
2 require("data.table", quietly = TRUE)
3 require("GEOquery", quietly = TRUE) 1 require("GEOquery", quietly = TRUE)
4 require("minfi", quietly = TRUE) 2 require("minfi", quietly = TRUE)
5 require("FDb.InfiniumMethylation.hg19", quietly = TRUE) 3 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
4
5 options(warn = -1)
6 options("download.file.method"="wget")
6 7
7 args <- commandArgs(trailingOnly = TRUE) 8 args <- commandArgs(trailingOnly = TRUE)
8 GSE = args[1] 9 GSE = args[1]
9 output = args[2] 10 output = args[2]
10 11
24 annotation = default.450k.annotation 25 annotation = default.450k.annotation
25 what = c("Beta", "M") 26 what = c("Beta", "M")
26 mergeManifest = FALSE 27 mergeManifest = FALSE
27 i = 1 28 i = 1
28 29
29 gset <- GEOquery::getGEO(GSE) 30 gset <- getGEO(GSE)
31
32 if (is.null(GSE)) {
33 stop("Must specify GSE")
34 } else {
35 options(download.file.method.GEOquery = "wget")}
36
30 gset <- gset[[1]] 37 gset <- gset[[1]]
31 38
32 platform <- annotation(gset) 39 platform <- annotation(gset)
33 40
34 ann <- getAnnotationString(c(array = array, annotation = annotation)) 41 ann <- getAnnotationString(c(array = array, annotation = annotation))