Merge pull request #758 from sneumann/quick_fix

small fixes

NAMESPACE

@@ -72,6 +72,7 @@ importMethodsFrom("MSnbase", "intensity", "mz", "rtime", "fileNames", "fromFile"
 importFrom("MSnbase", "as.data.frame.Spectrum", "Chromatogram",
     "MChromatograms", "MSpectra", "requiredFvarLabels", "selectFeatureData")
 
+
 export(
     "etg",
     "medianFilter",
@@ -254,7 +255,8 @@ export(
     "loadXcmsData",
     "matchLamasChromPeaks",
     "summarizeLamaMatch",
-    "matchedRtimes"
+    "matchedRtimes",
+    "XcmsExperiment"
 )
 
 ## New analysis methods
@@ -566,7 +568,7 @@ importMethodsFrom("Spectra", "precursorMz")
 importMethodsFrom("Spectra", "$")
 importMethodsFrom("Spectra", "uniqueMsLevels")
 importMethodsFrom("Spectra", "backendBpparam")
-importFrom("Spectra", "MsBackendMemory")
+importFrom("Spectra", "MsBackendMemory", "filterEmptySpectra")
 
 ## MsExperiment things
 importClassesFrom("MsExperiment", "MsExperiment")

R/XcmsExperiment-functions.R

@@ -1134,3 +1134,8 @@ featureArea <- function(object, mzmin = min, mzmax = max, rtmin = min,
         object@chromPeaks
     else chromPeaks(object@msFeatureData)
 }
+
+#' function to create an empty `XcmsExperiment` object
+XcmsExperiment <- function() {
+    as(MsExperiment(), "XcmsExperiment")
+}

R/XcmsExperiment-plotting.R

@@ -437,6 +437,9 @@ setMethod(
 #'
 #' @importFrom grDevices n2mfrow
 #'
+#' @importFrom Spectra filterEmptySpectra
+#'
+#'
 #' @export
 #'
 #' @author Johannes Rainer

R/XcmsExperiment.R

@@ -1450,7 +1450,9 @@ setMethod("dropAdjustedRtime", "XcmsExperiment", function(object) {
 
 #' @rdname XcmsExperiment
 setMethod("hasAdjustedRtime", "MsExperiment", function(object) {
-    any(spectraVariables(spectra(object)) == "rtime_adjusted")
+    if (length(spectra(object)))
+        any(spectraVariables(spectra(object)) == "rtime_adjusted")
+    else FALSE
 })
 
 #' @rdname XcmsExperiment