Mercurial > repos > testtool > geo_data
comparison GRsetFromGEO/GRsetFromGEO.R @ 37:c982fdb0e27d draft
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| author | testtool |
|---|---|
| date | Mon, 24 Apr 2017 08:57:06 -0400 |
| parents | b3761b109ca9 |
| children | 234e990e8e1d |
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| 36:b3761b109ca9 | 37:c982fdb0e27d |
|---|---|
| 19 | 19 |
| 20 default.450k.annotation <- "ilmn12.hg19" | 20 default.450k.annotation <- "ilmn12.hg19" |
| 21 | 21 |
| 22 | 22 |
| 23 | 23 |
| 24 function (GSE = GSE, array = "IlluminaHumanMethylation450k", annotation = default.450k.annotation, | 24 array = "IlluminaHumanMethylation450k" |
| 25 what = c("Beta", "M"), mergeManifest = FALSE, i = 1){ | 25 annotation = default.450k.annotation |
| 26 | 26 what = c("Beta", "M") |
| 27 | 27 mergeManifest = FALSE |
| 28 gset <- getGEO(GSE) | 28 i = 1 |
| 29 gset <- gset[[1]] | 29 |
| 30 | 30 gset <- getGEO(GSE) |
| 31 platform <- annotation(gset) | 31 gset <- gset[[1]] |
| 32 | 32 |
| 33 ann <- getAnnotationString(c(array = array, annotation = annotation)) | 33 platform <- annotation(gset) |
| 34 if (!require(ann, character.only = TRUE)) | 34 |
| 35 stop(sprintf("cannot load annotation package %s", ann)) | 35 ann <- getAnnotationString(c(array = array, annotation = annotation)) |
| 36 | 36 if (!require(ann, character.only = TRUE)) |
| 37 object <- get(ann) | 37 stop(sprintf("cannot load annotation package %s", ann)) |
| 38 | 38 |
| 39 gr <- getLocations(object, mergeManifest = mergeManifest, | 39 object <- get(ann) |
| 40 orderByLocation = TRUE) | 40 |
| 41 locusNames <- names(gr) | 41 gr <- getLocations(object, mergeManifest = mergeManifest, |
| 42 sampleNames(gset) <- gset$title | 42 orderByLocation = TRUE) |
| 43 common <- intersect(locusNames, fData(gset)$Name) | 43 locusNames <- names(gr) |
| 44 if (length(common) == 0) { | 44 sampleNames(gset) <- gset$title |
| 45 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.") | 45 common <- intersect(locusNames, fData(gset)$Name) |
| 46 ind1 <- match(common, fData(gset)$Name) | 46 if (length(common) == 0) { |
| 47 ind2 <- match(common, locusNames) | 47 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.") |
| 48 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details")) | 48 ind1 <- match(common, fData(gset)$Name) |
| 49 if (what == "Beta") { | 49 ind2 <- match(common, locusNames) |
| 50 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1, | 50 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details")) |
| 51 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset), | 51 if (what == "Beta") { |
| 52 annotation = c(array = array, annotation = annotation), | 52 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1, |
| 53 preprocessMethod = preprocessing) | 53 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset), |
| 54 } | 54 annotation = c(array = array, annotation = annotation), |
| 55 else { | 55 preprocessMethod = preprocessing) |
| 56 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL, | |
| 57 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL, | |
| 58 pData = pData(gset), annotation = c(array = array, | |
| 59 annotation = annotation), preprocessMethod = preprocessing) | |
| 60 } | |
| 61 return(out) | |
| 62 } | 56 } |
| 63 save(out,file = output) | 57 else { |
| 58 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL, | |
| 59 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL, | |
| 60 pData = pData(gset), annotation = c(array = array, | |
| 61 annotation = annotation), preprocessMethod = preprocessing) | |
| 62 } | |
| 63 return(out) | |
| 64 } | 64 } |
| 65 save(out,file = output) | |
| 66 | |
| 67 |