fix sanity check

R/AllGenerics.R

@@ -417,10 +417,10 @@ setGeneric("chromPeakData<-", function(object, value)
 #' spectra for one chromatographic peak (or a `Spectra` of length 0 if no
 #' spectrum was found for the respective chromatographic peak).
 #'
-#' Parameters `chromPeakColumns` allow the user to add specific metadata
+#' Parameter `chromPeakColumns` allows the user to add specific metadata
 #' columns from the chromatographic peaks (`chromPeaks`) to the returned
-#' spectra object. This can be useful to retain information such as retention
-#' time (`rt`), m/z (`mz`). The columns will be named as they is written in the
+#' spectra object. This can be useful to keep information such as retention
+#' time (`rt`), m/z (`mz`). The columns will be named as they are written in the
 #' `chromPeaks` object with the prefix `"chrom_peak_"`. The *peak ID*
 #' (i.e., the row name of the peak in the `chromPeaks` matrix) is always added
 #' to the spectra object as a metadata column named `"chrom_peak_id"`.
@@ -811,7 +811,7 @@ setGeneric("featureDefinitions<-", function(object, value)
 #'
 #' The information from `featureDefinitions` for each feature can be included
 #' in the returned [Spectra()] object using the `featureColumns` parameter.
-#' This is useful for retaining details such as the median retention time (`rtmed`)
+#' This is useful for keeping details such as the median retention time (`rtmed`)
 #' or median m/z (`mzmed`). The columns will retain their names as specified
 #' in the `featureDefinitions` object, prefixed by `"feature_"`
 #' (e.g., `"feature_mzmed"`). Additionally, the *feature ID* (i.e., the row

R/XcmsExperiment-functions.R

@@ -797,8 +797,12 @@
                                    chromPeakColumns = c("rt", "mz"),
                                    BPPARAM = bpparam()) {
     method <- match.arg(method)
-    pks <- .chromPeaks(x)[, c("mz", "mzmin", "mzmax", "rt",
-                              "rtmin", "rtmax", "maxo", "sample")]
+    if (!chromPeakColumns %in% colnames(.chromPeaks(x)))
+        stop("One or more of the columns in 'chromPeakColumns' are not ",
+             "available in the 'chromPeaks' data.")
+    pks <- .chromPeaks(x)[, union(c("mz", "mzmin", "mzmax", "rt",
+                              "rtmin", "rtmax", "maxo", "sample"),
+                              chromPeakColumns)]
     if (ppm != 0)
         expandMz <- expandMz + pks[, "mz"] * ppm / 1e6
     if (expandMz[1L] != 0) {

R/XcmsExperiment.R

@@ -1782,6 +1782,9 @@ setMethod(
         if (!hasFeatures(object))
             stop("No feature definitions present. Please run ",
                  "'groupChromPeaks' first.")
+        if (!featureColumns %in% colnames(featureDefinitions(object)))
+            stop("One or more of the requested 'featureColumns' are not ",
+                 "present in the feature definitions.")
         if (hasAdjustedRtime(object))
             object <- applyAdjustedRtime(object)
         features_all <- rownames(featureDefinitions(object))

tests/testthat/test_XcmsExperiment.R

@@ -939,6 +939,9 @@ test_that("chromPeakSpectra works", {
     expect_error(chromPeakSpectra(xmse, peaks = "other"), "out of bounds")
 
     pks <- c("CP242", "CP007", "CP123")
+
+    expect_error(chromPeakSpectra(xmse, peaks = pks,
+                                  chromPeakColumns = "other"), "not available")
     res <- chromPeakSpectra(xmse, peaks = pks)
     expect_s4_class(res, "Spectra")
     expect_equal(length(res), 0)
@@ -1081,6 +1084,8 @@ test_that("filterFeatureDefinitions works", {
 
 test_that("featureSpectra works", {
     expect_error(featureSpectra(xmse), "No feature definitions")
+    expect_error(featureSpectra(xmseg,
+                                  featureColumns = "other"), "not present")
     res_all <- featureSpectra(xmseg, msLevel = 1L)
     expect_s4_class(res_all, "Spectra")
     expect_true(all(rownames(featureDefinitions(xmseg)) %in%