version bump

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.5.0
+Version: 4.5.1
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,

NEWS.md

@@ -1,4 +1,15 @@
-# xcms 4.3
+# xcms 4.5
+
+## Changes in version 4.5.1
+
+- Small update to `featureSpectra()` and `chromPeakSpectra()` to allow addition
+  of `chromPeaks()` and `featuresDefinitions()` columns to be added to the
+  `Spectra` output. 
+- Tidied the `xcms` vignette, to order the filtering of features and remove 
+  the outdated normalisation paragraph.In depth discussion on this subject can 
+  be found on `metabonaut`. 
+
+# 4.3
 
 ## Changes in version 4.3.4
 
@@ -7,8 +18,6 @@
 - Small fix to the .yml file for the github actions, so they do not crash on 
   warnings.
 
-
-
 ## Changes in version 4.3.3
 
 - Fix issue #755: `chromatogram()` with `msLevel = 2` fails to extract

R/XcmsExperiment-functions.R

@@ -823,7 +823,7 @@
         split(spectra(x), factor(fromFile(x), levels = levels(f))),
         FUN = function(pk, sp, msLevel, method, addColumnsChromPeaks,
                        addColumnsChromPeaksPrefix) {
-            sp <- Spectra::filterMsLevel(sp, msLevel)
+            sp <- filterMsLevel(sp, msLevel)
             idx <- switch(
                 method,
                 all = .spectra_index_list(sp, pk, msLevel),
@@ -833,8 +833,9 @@
                 largest_bpi = .spectra_index_list_largest_bpi(sp, pk, msLevel))
             ids <- rep(rownames(pk), lengths(idx))
             res <- sp[unlist(idx)]
-            pk_data <- pk[ids, addColumnsChromPeaks, drop = FALSE]
-            pk_data <- cbind(pk_data, id = ids)
+            pk_data <- as.data.frame(pk[ids, addColumnsChromPeaks,
+                                        drop = FALSE])
+            pk_data$id <- ids
             colnames(pk_data) <- paste0(addColumnsChromPeaksPrefix,
                                           colnames(pk_data))
             res <- .add_spectra_data(res, pk_data)