diff lib-xcms3.x.x.r @ 0:c749bfd3410e draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib-xcms3.x.x.r	Tue Sep 18 16:06:05 2018 -0400
@@ -0,0 +1,152 @@
+
+
+#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
+# https://github.com/sneumann/xcms/issues/250
+groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
+    mzfmt <- paste("%.", mzdec, "f", sep = "")
+    rtfmt <- paste("%.", rtdec, "f", sep = "")
+
+    gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
+                    sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
+
+    if (any(dup <- duplicated(gnames)))
+        for (dupname in unique(gnames[dup])) {
+            dupidx <- which(gnames == dupname)
+            gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
+        }
+
+    return (gnames)
+}
+
+#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
+# https://github.com/sneumann/xcms/issues/247
+.concatenate_XCMSnExp <- function(...) {
+    x <- list(...)
+    if (length(x) == 0)
+        return(NULL)
+    if (length(x) == 1)
+        return(x[[1]])
+    ## Check that all are XCMSnExp objects.
+    if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
+        stop("All passed objects should be 'XCMSnExp' objects")
+    new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
+    ## If any of the XCMSnExp has alignment results or detected features drop
+    ## them!
+    x <- lapply(x, function(z) {
+        if (hasAdjustedRtime(z)) {
+            z <- dropAdjustedRtime(z)
+            warning("Adjusted retention times found, had to drop them.")
+        }
+        if (hasFeatures(z)) {
+            z <- dropFeatureDefinitions(z)
+            warning("Feature definitions found, had to drop them.")
+        }
+        z
+    })
+    ## Combine peaks
+    fls <- lapply(x, fileNames)
+    startidx <- cumsum(lengths(fls))
+    pks <- lapply(x, chromPeaks)
+    procH <- lapply(x, processHistory)
+    for (i in 2:length(fls)) {
+        pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
+        procH[[i]] <- lapply(procH[[i]], function(z) {
+            z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
+            z
+            })
+    }
+    pks <- do.call(rbind, pks)
+    new_x@.processHistory <- unlist(procH)
+    chromPeaks(new_x) <- pks
+    if (validObject(new_x))
+        new_x
+}
+
+#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
+# https://github.com/sneumann/xcms/issues/247
+.concatenate_OnDiskMSnExp <- function(...) {
+    x <- list(...)
+    if (length(x) == 0)
+        return(NULL)
+    if (length(x) == 1)
+        return(x[[1]])
+    ## Check that all are XCMSnExp objects.
+    if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
+        stop("All passed objects should be 'OnDiskMSnExp' objects")
+    ## Check processingQueue
+    procQ <- lapply(x, function(z) z@spectraProcessingQueue)
+    new_procQ <- procQ[[1]]
+    is_ok <- unlist(lapply(procQ, function(z)
+        !is.character(all.equal(new_procQ, z))
+        ))
+    if (any(!is_ok)) {
+        warning("Processing queues from the submitted objects differ! ",
+                "Dropping the processing queue.")
+        new_procQ <- list()
+    }
+    ## processingData
+    fls <- lapply(x, function(z) z@processingData@files)
+    startidx <- cumsum(lengths(fls))
+    ## featureData
+    featd <- lapply(x, fData)
+    ## Have to update the file index and the spectrum names.
+    for (i in 2:length(featd)) {
+        featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
+        rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
+                                              fileIds = featd[[i]]$fileIdx,
+                                              spectrumIds = featd[[i]]$spIdx,
+                                              nSpectra = nrow(featd[[i]]),
+                                              nFiles = length(unlist(fls))
+                                          )
+    }
+    featd <- do.call(rbind, featd)
+    featd$spectrum <- 1:nrow(featd)
+    ## experimentData
+    expdata <- lapply(x, function(z) {
+        ed <- z@experimentData
+        data.frame(instrumentManufacturer = ed@instrumentManufacturer,
+                   instrumentModel = ed@instrumentModel,
+                   ionSource = ed@ionSource,
+                   analyser = ed@analyser,
+                   detectorType = ed@detectorType,
+                   stringsAsFactors = FALSE)
+    })
+    expdata <- do.call(rbind, expdata)
+    expdata <- new("MIAPE",
+                   instrumentManufacturer = expdata$instrumentManufacturer,
+                   instrumentModel = expdata$instrumentModel,
+                   ionSource = expdata$ionSource,
+                   analyser = expdata$analyser,
+                   detectorType = expdata$detectorType)
+
+    ## protocolData
+    protodata <- lapply(x, function(z) z@protocolData)
+    if (any(unlist(lapply(protodata, nrow)) > 0))
+        warning("Found non-empty protocol data, but merging protocol data is",
+                " currently not supported. Skipped.")
+    ## phenoData
+    pdata <- do.call(rbind, lapply(x, pData))
+    res <- new(
+        "OnDiskMSnExp",
+        phenoData = new("NAnnotatedDataFrame", data = pdata),
+        featureData = new("AnnotatedDataFrame", featd),
+        processingData = new("MSnProcess",
+                             processing = paste0("Concatenated [", date(), "]"),
+                             files = unlist(fls), smoothed = NA),
+        experimentData = expdata,
+        spectraProcessingQueue = new_procQ)
+    if (validObject(res))
+        res
+}
+
+#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
+# https://github.com/sneumann/xcms/issues/247
+c.XCMSnExp <- function(...) {
+    .concatenate_XCMSnExp(...)
+}
+
+#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
+# https://github.com/sneumann/xcms/issues/247
+c.MSnbase <- function(...) {
+    .concatenate_OnDiskMSnExp(...)
+}