Mercurial > repos > lecorguille > xcms_fillpeaks

annotate lib-xcms3.x.x.r @ 38:a3e80894efd3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
author lecorguille
date Mon, 17 Sep 2018 08:46:47 -0400
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38
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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1
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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2
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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3 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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4 # https://github.com/sneumann/xcms/issues/250
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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5 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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6 mzfmt <- paste("%.", mzdec, "f", sep = "")
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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7 rtfmt <- paste("%.", rtdec, "f", sep = "")
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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8
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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9 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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10 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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11
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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12 if (any(dup <- duplicated(gnames)))
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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13 for (dupname in unique(gnames[dup])) {
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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14 dupidx <- which(gnames == dupname)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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15 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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16 }
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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17
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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18 return (gnames)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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19 }
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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20
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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21 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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22 # https://github.com/sneumann/xcms/issues/247
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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23 .concatenate_XCMSnExp <- function(...) {
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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24 x <- list(...)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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25 if (length(x) == 0)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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26 return(NULL)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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27 if (length(x) == 1)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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28 return(x[[1]])
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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29 ## Check that all are XCMSnExp objects.
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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30 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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31 stop("All passed objects should be 'XCMSnExp' objects")
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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32 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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33 ## If any of the XCMSnExp has alignment results or detected features drop
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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34 ## them!
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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35 x <- lapply(x, function(z) {
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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36 if (hasAdjustedRtime(z)) {
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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37 z <- dropAdjustedRtime(z)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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38 warning("Adjusted retention times found, had to drop them.")
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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39 }
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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40 if (hasFeatures(z)) {
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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41 z <- dropFeatureDefinitions(z)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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42 warning("Feature definitions found, had to drop them.")
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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43 }
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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44 z
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45 })
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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46 ## Combine peaks
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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47 fls <- lapply(x, fileNames)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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48 startidx <- cumsum(lengths(fls))
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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49 pks <- lapply(x, chromPeaks)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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50 procH <- lapply(x, processHistory)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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51 for (i in 2:length(fls)) {
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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52 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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53 procH[[i]] <- lapply(procH[[i]], function(z) {
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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54 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
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55 z
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56 })
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57 }
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58 pks <- do.call(rbind, pks)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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59 new_x@.processHistory <- unlist(procH)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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60 chromPeaks(new_x) <- pks
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61 if (validObject(new_x))
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62 new_x
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63 }
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64
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65 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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66 # https://github.com/sneumann/xcms/issues/247
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67 .concatenate_OnDiskMSnExp <- function(...) {
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68 x <- list(...)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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69 if (length(x) == 0)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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70 return(NULL)
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71 if (length(x) == 1)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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72 return(x[[1]])
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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73 ## Check that all are XCMSnExp objects.
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74 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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75 stop("All passed objects should be 'OnDiskMSnExp' objects")
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76 ## Check processingQueue
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77 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
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78 new_procQ <- procQ[[1]]
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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79 is_ok <- unlist(lapply(procQ, function(z)
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80 !is.character(all.equal(new_procQ, z))
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81 ))
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82 if (any(!is_ok)) {
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83 warning("Processing queues from the submitted objects differ! ",
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84 "Dropping the processing queue.")
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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85 new_procQ <- list()
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86 }
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87 ## processingData
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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88 fls <- lapply(x, function(z) z@processingData@files)
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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89 startidx <- cumsum(lengths(fls))
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90 ## featureData
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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91 featd <- lapply(x, fData)
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92 ## Have to update the file index and the spectrum names.
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93 for (i in 2:length(featd)) {
a3e80894efd3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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94 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
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95 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
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96 fileIds = featd[[i]]$fileIdx,
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97 spectrumIds = featd[[i]]$spIdx,
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98 nSpectra = nrow(featd[[i]]),
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99 nFiles = length(unlist(fls))
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100 )
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101 }
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102 featd <- do.call(rbind, featd)
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103 featd$spectrum <- 1:nrow(featd)
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104 ## experimentData
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105 expdata <- lapply(x, function(z) {
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106 ed <- z@experimentData
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107 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
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108 instrumentModel = ed@instrumentModel,
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109 ionSource = ed@ionSource,
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110 analyser = ed@analyser,
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111 detectorType = ed@detectorType,
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112 stringsAsFactors = FALSE)
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113 })
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114 expdata <- do.call(rbind, expdata)
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115 expdata <- new("MIAPE",
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116 instrumentManufacturer = expdata$instrumentManufacturer,
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117 instrumentModel = expdata$instrumentModel,
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118 ionSource = expdata$ionSource,
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119 analyser = expdata$analyser,
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120 detectorType = expdata$detectorType)
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121
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122 ## protocolData
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123 protodata <- lapply(x, function(z) z@protocolData)
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124 if (any(unlist(lapply(protodata, nrow)) > 0))
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125 warning("Found non-empty protocol data, but merging protocol data is",
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126 " currently not supported. Skipped.")
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127 ## phenoData
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128 pdata <- do.call(rbind, lapply(x, pData))
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129 res <- new(
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130 "OnDiskMSnExp",
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131 phenoData = new("NAnnotatedDataFrame", data = pdata),
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132 featureData = new("AnnotatedDataFrame", featd),
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133 processingData = new("MSnProcess",
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134 processing = paste0("Concatenated [", date(), "]"),
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135 files = unlist(fls), smoothed = NA),
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136 experimentData = expdata,
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137 spectraProcessingQueue = new_procQ)
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138 if (validObject(res))
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139 res
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140 }
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141
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142 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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143 # https://github.com/sneumann/xcms/issues/247
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144 c.XCMSnExp <- function(...) {
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145 .concatenate_XCMSnExp(...)
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146 }
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147
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148 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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149 # https://github.com/sneumann/xcms/issues/247
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150 c.MSnbase <- function(...) {
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151 .concatenate_OnDiskMSnExp(...)
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152 }