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42
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1 require("GEOquery", quietly = TRUE)
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34
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2 require("minfi", quietly = TRUE)
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36
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3 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
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34
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4
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43
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5 options(warn = -1)
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6 options("download.file.method"="wget")
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7
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34
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8 args <- commandArgs(trailingOnly = TRUE)
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9 GSE = args[1]
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10 output = args[2]
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11
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36
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12 getAnnotationString <- function(annotation) {
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13 if(length(annotation) == 1)
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14 return(sprintf("%sanno", annotation))
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15 if(all(c("array", "annotation") %in% names(annotation)))
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16 return(sprintf("%sanno.%s", annotation["array"], annotation["annotation"]))
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17 stop("unable to get the annotation string for this object")
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18 }
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19
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20 default.450k.annotation <- "ilmn12.hg19"
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21
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22
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23
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37
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24 array = "IlluminaHumanMethylation450k"
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25 annotation = default.450k.annotation
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26 what = c("Beta", "M")
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27 mergeManifest = FALSE
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28 i = 1
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29
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43
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30 gset <- getGEO(GSE)
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31
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32 if (is.null(GSE)) {
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33 stop("Must specify GSE")
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34 } else {
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35 options(download.file.method.GEOquery = "wget")}
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36
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37
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37 gset <- gset[[1]]
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38
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39 platform <- annotation(gset)
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40
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41 ann <- getAnnotationString(c(array = array, annotation = annotation))
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42 if (!require(ann, character.only = TRUE))
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43 stop(sprintf("cannot load annotation package %s", ann))
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44
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45 object <- get(ann)
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46
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47 gr <- getLocations(object, mergeManifest = mergeManifest,
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48 orderByLocation = TRUE)
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49 locusNames <- names(gr)
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50 sampleNames(gset) <- gset$title
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51 common <- intersect(locusNames, fData(gset)$Name)
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52 if (length(common) == 0) {
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53 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
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54 ind1 <- match(common, fData(gset)$Name)
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55 ind2 <- match(common, locusNames)
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56 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
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57 if (what == "Beta") {
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58 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
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59 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
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60 annotation = c(array = array, annotation = annotation),
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61 preprocessMethod = preprocessing)
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35
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62 }
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37
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63 else {
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64 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
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65 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
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66 pData = pData(gset), annotation = c(array = array,
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67 annotation = annotation), preprocessMethod = preprocessing)
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68 }
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69 return(out)
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35
|
70 }
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37
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71 save(out,file = output)
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72
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73
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