Add parameter groupnames to exportMetaboAnalyst

- Add parameter groupnames to exportMetaboAnalyst to allow using m/z and
  retention times as rownames (issue #296).
- Fix bug in `show,XCMSnExp` that would lead to an error if process history is
  empty.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: xcms
-Version: 3.5.0
-Date: 2018-10-26
+Version: 3.5.1
+Date: 2018-11-05
 Title: LC/MS and GC/MS Data Analysis
 Author: Colin A. Smith <csmith@scripps.edu>,
     Ralf Tautenhahn <rtautenh@gmail.com>,

R/functions-XCMSnExp.R

@@ -1808,6 +1808,12 @@ overlappingFeatures <- function(x, expandMz = 0, expandRt = 0, ppm = 0) {
 #' @param digits `integer(1)` defining the number of significant digits to be
 #'     used for numeric. The default `NULL` uses `getOption("digits")`. See
 #'     [format()] for more information.
+#'
+#' @param groupnames `logical(1)` whether row names of the resulting matrix
+#'     should be the feature IDs (`groupnames = FALSE`; default) or IDs that
+#'     are composed of the m/z and retention time of the features (in the
+#'     format *M<m/z>T<rt>* (`groupnames = TRUE`). See help of the [groupnames]
+#'     function for details.
 #' 
 #' @param ... additional parameters to be passed to the [featureValues()]
 #'     function.
@@ -1821,7 +1827,8 @@ overlappingFeatures <- function(x, expandMz = 0, expandRt = 0, ppm = 0) {
 #'
 #' @md
 exportMetaboAnalyst <- function(x, file = NULL, label,
-                                value = "into", digits = NULL, ...) {
+                                value = "into", digits = NULL,
+                                groupnames = FALSE, ...) {
     if (!is(x, "XCMSnExp"))
         stop("'x' is supposed to be an XCMSnExp object")
     fv <- featureValues(x, value = value, ...)
@@ -1831,6 +1838,8 @@ exportMetaboAnalyst <- function(x, file = NULL, label,
     if (missing(label))
         stop("Please provide the group assignment of the samples with the ",
              "'label' parameter")
+    if (groupnames)
+        rownames(fv) <- groupnames(x)
     if (length(label) == 1) {
         if (any(colnames(pData(x)) == label))
             label <- as.character(pData(x)[, label])

R/methods-XCMSnExp.R

@@ -20,7 +20,9 @@ setMethod("show", "XCMSnExp", function(object) {
     if (hasChromPeaks(object)) {
         cat("Chromatographic peak detection:\n")
         ph <- processHistory(object, type = .PROCSTEP.PEAK.DETECTION)
-        cat(" method:", .param2string(ph[[1]]@param), "\n")
+        if (length(ph))
+            cat(" method:", .param2string(ph[[1]]@param), "\n")
+        else cat(" unknown method.\n")
         cat(" ", nrow(chromPeaks(object)), " peaks identified in ",
             length(fileNames(object)), " samples.\n", sep = "")
         cat(" On average ",
@@ -30,12 +32,16 @@ setMethod("show", "XCMSnExp", function(object) {
     if (hasAdjustedRtime(object)) {
         cat("Alignment/retention time adjustment:\n")
         ph <- processHistory(object, type = .PROCSTEP.RTIME.CORRECTION)
-        cat(" method:", .param2string(ph[[1]]@param), "\n")
+        if (length(ph))
+            cat(" method:", .param2string(ph[[1]]@param), "\n")
+        else cat(" unknown method.\n")
     }
     if (hasFeatures(object)) {
         cat("Correspondence:\n")
         ph <- processHistory(object, type = .PROCSTEP.PEAK.GROUPING)
-        cat(" method:", .param2string(ph[[1]]@param), "\n")
+        if (length(ph))
+            cat(" method:", .param2string(ph[[1]]@param), "\n")
+        else cat(" unknown method.\n")
         cat(" ", nrow(featureDefinitions(object)), " features identified.\n",
             sep = "")
         cat(" Median mz range of features: ",

inst/NEWS

@@ -1,3 +1,10 @@
+Changes in version 3.5.1
+
+- Add parameter groupval to exportMetaboAnalyst (issue #296).
+- Fix bug in show,XCMSnExp that would throw an error if no process history is
+  present.
+
+
 Changes in version 3.3.6
 
 - Add type = "polygon" to highlightChromPeaks allowing to fill the actual

tests/testthat/test_functions-XCMSnExp.R

@@ -207,6 +207,10 @@ test_that("exportMetaboAnalyst works", {
     res3 <- read.table(fl, sep = ",", row.names = 1, as.is = TRUE)
     colnames(res3) <- colnames(res)
     expect_equal(as.matrix(res3), res)
+
+    res <- exportMetaboAnalyst(xod_xg, label = c("a", "a", "a"),
+                               groupnames = TRUE)
+    expect_equal(rownames(res), c("Sample", "Label", groupnames(xod_xg)))
 })
 
 test_that("chromPeakSpectra works", {