comparison getGEO.R @ 2:556ebcea6989 draft

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author testtool
date Wed, 18 Jan 2017 10:13:19 -0500
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1:1ab7612c5107 2:556ebcea6989
1 require("BiocGenerics", quietly = TRUE)
2 require("data.table", quietly = TRUE)
3 require("GEOquery", quietly = TRUE)
4 require("rtracklayer", quietly = TRUE)
5 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
6
7 options(warn = -1)
8 args <- commandArgs(trailingOnly = TRUE)
9 GSMTable = args[1]
10 MetaTable = args[2]
11 IlmnTable = args[3]
12 gmTable = args[4]
13
14 TAB = fread(GSMTable)
15
16 if (is.null(TAB)) {
17 stop("Must specify input files")
18 } else {
19 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
20 IlmnIDTable <- Table(GEODataTable)
21 MetaData <- data.frame(Meta(GEODataTable))
22
23
24 write.csv(MetaData, MetaTable, row.names = FALSE, sep = "\t")
25 }
26
27 hm450.hg19 <- getPlatform()
28
29 IlmnInfo <-
30 data.table(
31 IlmnID = names(hm450.hg19),
32 CHR = as.data.frame(hm450.hg19@seqnames)$value,
33 BP = as.numeric(hm450.hg19@elementMetadata$probeStart)
34 )
35
36
37 write.csv(IlmnInfo, IlmnTable, row.names = FALSE, sep = "\t")
38
39
40 if (length(TAB$ID) > 1) {
41 mysamples <-
42 do.call("data.table", lapply(TAB$ID[-1], function(x)
43 Table(getGEO(x, getGPL = FALSE))[, -1]))
44
45 gmSet <- data.table(IlmnIDTable[, -1], mysamples)
46
47 } else {
48 gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE))
49 }
50
51
52 write.csv(gmSet, gmTable, row.names = FALSE, sep = "\t")