Addition of method to filter features based on quality assessment

sneumann · Jan 24, 2024 · 3815295 · 3815295
1 parent 548c248
commit 3815295
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.1.5
+Version: 4.1.6
 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,
@@ -87,7 +87,7 @@ URL: https://github.com/sneumann/xcms
 BugReports: https://github.com/sneumann/xcms/issues/new
 VignetteBuilder: knitr
 biocViews: ImmunoOncology, MassSpectrometry, Metabolomics
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Collate:
     'AllGenerics.R'
     'functions-XChromatograms.R'
@@ -127,6 +127,7 @@ Collate:
     'init.R'
     'loadXcmsData.R'
     'matchpeaks.R'
+    'method-filterFeatures.R'
     'methods-Chromatogram.R'
     'methods-IO.R'
     'methods-MChromatograms.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -4,7 +4,7 @@ importFrom("utils", "capture.output", "data")
 import("methods")
 importMethodsFrom("ProtGenerics", "peaks", "chromatogram", "writeMSData",
     "polarity<-", "centroided", "isCentroided", "peaks<-",
-    "isolationWindowTargetMz", "quantify", "bin", "spectrapply")
+    "isolationWindowTargetMz", "quantify", "bin", "spectrapply", "filterFeatures")
 importClassesFrom("ProtGenerics", "Param")
 importFrom("BiocGenerics", "updateObject", "fileName", "subset",
     "dirname", "dirname<-")
@@ -594,3 +594,8 @@ export("RDataParam")
 export("PlainTextParam")
 exportMethods("storeResults")
 
+## filtering features things
+export("RsdFilter")
+export("DratioFilter")
+export("PercentMissingFilter")
+export("BlankFlag")
diff --git a/R/DataClasses.R b/R/DataClasses.R
@@ -190,6 +190,7 @@ setClass("xcmsPeaks", contains = "matrix")
 .PROCSTEP.PEAK.FILLING <- "Missing peak filling"
 .PROCSTEP.CALIBRATION <- "Calibration"
 .PROCSTEP.FEATURE.GROUPING <- "Feature grouping"
+.PROCSTEP.FEATURE.FILTERING <- "Feature filtering"
 .PROCSTEPS <- c(
     .PROCSTEP.UNKNOWN,
     .PROCSTEP.PEAK.DETECTION,
@@ -198,7 +199,8 @@ setClass("xcmsPeaks", contains = "matrix")
     .PROCSTEP.RTIME.CORRECTION,
     .PROCSTEP.PEAK.FILLING,
     .PROCSTEP.CALIBRATION,
-    .PROCSTEP.FEATURE.GROUPING
+    .PROCSTEP.FEATURE.GROUPING,
+    .PROCSTEP.FEATURE.FILTERING
 )
 
 ############################################################