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comparison GRsetFromGEO/GRsetFromGEO.R @ 35:694382fd220a draft

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Uploaded
author testtool
date Fri, 14 Apr 2017 14:16:46 -0400
parents 59a5237b72a3
children b3761b109ca9
comparison
equal deleted inserted replaced
34:59a5237b72a3 35:694382fd220a
2 2
3 args <- commandArgs(trailingOnly = TRUE) 3 args <- commandArgs(trailingOnly = TRUE)
4 GSE = args[1] 4 GSE = args[1]
5 output = args[2] 5 output = args[2]
6 6
7 GRset <- getGenomicRatioSetFromGEO(GSE) 7 function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
8 8 annotation = .default.450k.annotation, what = c("Beta", "M"),
9 save(GRset,output) 9 mergeManifest = FALSE, i = 1)
10 {
11 what <- match.arg(what)
12 if (is.null(GSE) && is.null(path))
13 stop("Either GSE or path must be supplied.")
14 if (!is.null(GSE))
15 gset <- GEOquery::getGEO(GSE)
16 else gset <- GEOquery::getGEO(filename = file.path(path,
17 list.files(path, pattern = ".soft")))
18 if (length(gset) == 0)
19 stop("Empty list retrieved from GEO.")
20 if (length(gset) > 1) {
21 warning("More than one ExpressionSet found:\n", names(gset),
22 "\nUsing entry ", i)
23 gset <- gset[[i]]
24 }
25 else gset <- gset[[1]]
26 platform <- annotation(gset)
27 if (platform != "GPL13534")
28 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
29 platform))
30 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
31 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
32 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
33 ann <- .getAnnotationString(c(array = array, annotation = annotation))
34 if (!require(ann, character.only = TRUE))
35 stop(sprintf("cannot load annotation package %s", ann))
36 object <- get(ann)
37 gr <- getLocations(object, mergeManifest = mergeManifest,
38 orderByLocation = TRUE)
39 locusNames <- names(gr)
40 sampleNames(gset) <- gset$title
41 common <- intersect(locusNames, fData(gset)$Name)
42 if (length(common) == 0)
43 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
44 ind1 <- match(common, fData(gset)$Name)
45 ind2 <- match(common, locusNames)
46 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
47 if (what == "Beta") {
48 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
49 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
50 annotation = c(array = array, annotation = annotation),
51 preprocessMethod = preprocessing)
52 }
53 else {
54 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
55 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
56 pData = pData(gset), annotation = c(array = array,
57 annotation = annotation), preprocessMethod = preprocessing)
58 }
59 save(out,output)
60 }