Mercurial > repos > testtool > geo_data
comparison getGEO/getGEO.R @ 54:7aab6e28c62e draft
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| author | testtool |
|---|---|
| date | Tue, 25 Apr 2017 10:28:34 -0400 |
| parents | cbc8174bd361 |
| children | fc93085430a8 |
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| 53:46acdba0f6d8 | 54:7aab6e28c62e |
|---|---|
| 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("download.file.method.GEOquery"="wget") | |
| 8 options(warn = -1) | |
| 9 | |
| 10 args <- commandArgs(trailingOnly = TRUE) | |
| 11 GSMTable = args[1] | |
| 12 protocol = args[2] | |
| 13 platform = args[3] | |
| 14 Data_Table = args[4] | |
| 15 | |
| 16 TAB = fread(GSMTable) | |
| 17 | |
| 18 if (is.null(TAB)) { | |
| 19 stop("Must specify input files") | |
| 20 } else { | |
| 21 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE) | |
| 22 IlmnIDTable <- Table(GEODataTable) | |
| 23 MetaData <- data.frame(Meta(GEODataTable)) | |
| 24 | |
| 25 | |
| 26 write.table(MetaData, protocol, row.names = FALSE, sep = "\t") | |
| 27 } | |
| 28 | |
| 29 hm450.hg19 <- getPlatform() | |
| 30 | |
| 31 IlmnInfo <- | |
| 32 data.table( | |
| 33 IlmnID = names(hm450.hg19), | |
| 34 CHR = as.data.frame(hm450.hg19@seqnames)$value, | |
| 35 BP = as.numeric(hm450.hg19@elementMetadata$probeStart) | |
| 36 ) | |
| 37 | |
| 38 | |
| 39 write.table(IlmnInfo, platform, row.names = FALSE, sep = "\t") | |
| 40 | |
| 41 | |
| 42 if (length(TAB$ID) > 1) { | |
| 43 mysamples <- | |
| 44 do.call("data.table", lapply(TAB$ID[-1], function(x) | |
| 45 Table(getGEO(x, getGPL = FALSE))[, -1])) | |
| 46 | |
| 47 gmSet <- data.table(IlmnIDTable[, -1], mysamples) | |
| 48 | |
| 49 } else { | |
| 50 gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE)) | |
| 51 } | |
| 52 | |
| 53 write.table(gmSet, Data_Table, row.names = FALSE,quote=FALSE,sep="\t") | |
| 54 |