Addition of method to filter features based on quality assessment

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.1.6
+Version: 4.1.7
 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,
@@ -62,7 +62,8 @@ Imports:
  Spectra (>= 1.13.2),
  progress,
  multtest,
- jsonlite
+ jsonlite,
+ MetaboCoreUtils (>= 1.11.2)
 Suggests:
  BiocStyle,
  caTools,
@@ -76,7 +77,6 @@ Suggests:
  MALDIquant,
  pheatmap,
  MsBackendMgf,
- MetaboCoreUtils,
  signal
 Enhances:
  Rgraphviz,
@@ -127,6 +127,7 @@ Collate:
  'init.R'
  'loadXcmsData.R'
  'matchpeaks.R'
+ 'method-filterFeatures.R'
  'methods-Chromatogram.R'
  'methods-IO.R'
  'methods-MChromatograms.R'

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<-")
@@ -35,6 +35,9 @@ importFrom("S4Vectors", "split", "Rle", "DataFrame", "SimpleList", "List",
 importMethodsFrom("S4Vectors", "as.matrix", "mcols", "mcols<-",
  "extractROWS", "findMatches")
 importFrom("SummarizedExperiment", "SummarizedExperiment")
+importFrom("SummarizedExperiment", "rowData")
+importFrom("SummarizedExperiment", "rowData<-")
+importFrom("SummarizedExperiment", "assay")
 importFrom("MsCoreUtils", "rbindFill", "closest", "i2index", "sumi", "between",
  "maxi", "breaks_ppm")
 
@@ -594,3 +597,11 @@ importFrom("jsonlite", "serializeJSON", "write_json", "unserializeJSON",
 export("RDataParam")
 export("PlainTextParam")
 exportMethods("storeResults")
+
+## filtering features things
+importFrom("MetaboCoreUtils", "rowRsd", "rowDratio", "rowPercentMissing",
+ "rowBlank")
+export("RsdFilter")
+export("DratioFilter")
+export("PercentMissingFilter")
+export("BlankFlag")

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
 )
 
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