Merge branch 'devel' into jomain

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,
@@ -46,7 +46,7 @@ Imports:
     methods,
     Biobase,
     BiocGenerics,
-    ProtGenerics (>= 1.29.1),
+    ProtGenerics (>= 1.35.2),
     lattice,
     RColorBrewer,
     plyr,
@@ -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
 )
 
 ############################################################