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42
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1 require("BiocGenerics", quietly = TRUE)
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2 require("data.table", quietly = TRUE)
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3 require("GEOquery", quietly = TRUE)
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34
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4 require("minfi", quietly = TRUE)
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36
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5 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
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34
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6
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7 args <- commandArgs(trailingOnly = TRUE)
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8 GSE = args[1]
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9 output = args[2]
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10
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36
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11 getAnnotationString <- function(annotation) {
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12 if(length(annotation) == 1)
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13 return(sprintf("%sanno", annotation))
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14 if(all(c("array", "annotation") %in% names(annotation)))
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15 return(sprintf("%sanno.%s", annotation["array"], annotation["annotation"]))
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16 stop("unable to get the annotation string for this object")
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17 }
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18
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19 default.450k.annotation <- "ilmn12.hg19"
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20
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21
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22
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37
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23 array = "IlluminaHumanMethylation450k"
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24 annotation = default.450k.annotation
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25 what = c("Beta", "M")
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26 mergeManifest = FALSE
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27 i = 1
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28
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42
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29 gset <- GEOquery::getGEO(GSE)
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37
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30 gset <- gset[[1]]
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31
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32 platform <- annotation(gset)
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33
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34 ann <- getAnnotationString(c(array = array, annotation = annotation))
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35 if (!require(ann, character.only = TRUE))
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36 stop(sprintf("cannot load annotation package %s", ann))
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37
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38 object <- get(ann)
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39
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40 gr <- getLocations(object, mergeManifest = mergeManifest,
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41 orderByLocation = TRUE)
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42 locusNames <- names(gr)
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43 sampleNames(gset) <- gset$title
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44 common <- intersect(locusNames, fData(gset)$Name)
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45 if (length(common) == 0) {
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46 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
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47 ind1 <- match(common, fData(gset)$Name)
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48 ind2 <- match(common, locusNames)
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49 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
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50 if (what == "Beta") {
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51 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
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52 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
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53 annotation = c(array = array, annotation = annotation),
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54 preprocessMethod = preprocessing)
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35
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55 }
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37
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56 else {
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57 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
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58 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
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59 pData = pData(gset), annotation = c(array = array,
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60 annotation = annotation), preprocessMethod = preprocessing)
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61 }
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62 return(out)
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35
|
63 }
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37
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64 save(out,file = output)
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65
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66
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