fix: fix bug in filterFeatures,PercentMissingFilter

sneumann · Feb 23, 2024 · e606322 · e606322
1 parent 1cf7cda
commit e606322
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Showing 3 changed files with 8 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.1.7
+Version: 4.1.8
 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,

diff --git a/R/method-filterFeatures.R b/R/method-filterFeatures.R
@@ -455,7 +455,7 @@ setMethod("filterFeatures",
                   vals <- rowPercentMissing(featureValues(object, ...)[, spl_idx])
                   fts_idx <- c(fts_idx, which(vals <= filter@threshold))
               }
-              fts_idx <- order(unique(fts_idx))
+              fts_idx <- sort(unique(fts_idx))
               message(length(vals) - length(fts_idx), " features were removed")
               ph <- XProcessHistory(param = filter,
                                     date. = date(),
@@ -479,7 +479,7 @@ setMethod("filterFeatures",
                   vals <- rowPercentMissing(assay(object, assay)[, spl_idx])
                   fts_idx <- c(fts_idx, which(vals <= filter@threshold))
               }
-              fts_idx <- order(unique(fts_idx))
+              fts_idx <- sort(unique(fts_idx))
               message(length(vals) - length(fts_idx), " features were removed")
               object[fts_idx]
           }

diff --git a/inst/NEWS b/inst/NEWS
@@ -1,3 +1,8 @@
+Changes in version 4.1.8
+----------------------
+
+- Fix bug in `filterFeatures,PercentMissingFilter`.
+
 Changes in version 4.1.7
 ----------------------