Mercurial > repos > testtool > get_geo
comparison getGEO/getGEO.R @ 22:fe105dbd7e1e draft
Uploaded
| author | testtool |
|---|---|
| date | Mon, 06 Feb 2017 09:23:31 -0500 |
| parents | |
| children | b342a87d7c03 |
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| 21:9746b310d9ad | 22:fe105dbd7e1e |
|---|---|
| 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 options("download.file.method"="wget") | |
| 9 args <- commandArgs(trailingOnly = TRUE) | |
| 10 GSMTable = args[1] | |
| 11 MetaTable = args[2] | |
| 12 IlmnTable = args[3] | |
| 13 gmTable = args[4] | |
| 14 | |
| 15 TAB = fread(GSMTable) | |
| 16 | |
| 17 if (is.null(TAB)) { | |
| 18 stop("Must specify input files") | |
| 19 } else { | |
| 20 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE) | |
| 21 IlmnIDTable <- Table(GEODataTable) | |
| 22 MetaData <- data.frame(Meta(GEODataTable)) | |
| 23 | |
| 24 | |
| 25 write.csv(MetaData, MetaTable, row.names = FALSE, sep = "\t") | |
| 26 } | |
| 27 | |
| 28 hm450.hg19 <- getPlatform() | |
| 29 | |
| 30 IlmnInfo <- | |
| 31 data.table( | |
| 32 IlmnID = names(hm450.hg19), | |
| 33 CHR = as.data.frame(hm450.hg19@seqnames)$value, | |
| 34 BP = as.numeric(hm450.hg19@elementMetadata$probeStart) | |
| 35 ) | |
| 36 | |
| 37 | |
| 38 write.csv(IlmnInfo, IlmnTable, row.names = FALSE, sep = "\t") | |
| 39 | |
| 40 | |
| 41 if (length(TAB$ID) > 1) { | |
| 42 mysamples <- | |
| 43 do.call("data.table", lapply(TAB$ID[-1], function(x) | |
| 44 Table(getGEO(x, getGPL = FALSE))[, -1])) | |
| 45 | |
| 46 gmSet <- data.table(IlmnIDTable[, -1], mysamples) | |
| 47 | |
| 48 } else { | |
| 49 gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE)) | |
| 50 } | |
| 51 | |
| 52 | |
| 53 write.csv(gmSet, gmTable, row.names = FALSE, sep = "\t") |