Merged xcms3 by Johannes Rainer

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@126426 bc3139a8-67e5-0310-9ffc-ced21a209358
sneumann · Feb 3, 2017 · 84eee36 · 84eee36
1 parent 283023b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: xcms
-Version: 1.51.4
-Date: 2017-01-16
+Version: 1.51.6
+Date: 2017-02-03
 Title: LC/MS and GC/MS Data Analysis
 Author: Colin A. Smith <csmith@scripps.edu>,
     Ralf Tautenhahn <rtautenh@gmail.com>,
@@ -16,15 +16,15 @@ Depends:
     BiocGenerics,
     ProtGenerics,
     Biobase,
-    MSnbase (>= 2.1.4)
+    MSnbase (>= 2.1.10)
 Imports:
     lattice,
     RColorBrewer,
     plyr,
     RANN,
     multtest,
     MassSpecWavelet (>= 1.5.2),
-    BiocParallel,
+    BiocParallel (>= 1.8.0),
     S4Vectors
 Suggests:
     BiocStyle,
@@ -54,14 +54,16 @@ Collate:
     'c.R'
     'cwTools.R'
     'databases.R'
+    'functions-MsFeatureData.R'
+    'do_adjustRtime-functions.R'
     'functions-binning.R'
     'do_detectFeatures-functions.R'
+    'functions-Params.R'
+    'do_groupFeatures-functions.R'
     'fastMatch.R'
     'functions-utils.R'
     'functions-IO.R'
-    'functions-MsFeatureData.R'
     'functions-OnDiskMSnExp.R'
-    'functions-Params.R'
     'functions-ProcessHistory.R'
     'functions-XCMSnExp.R'
     'functions-xcmsEIC.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -12,8 +12,10 @@ importFrom("plyr", "rbind.fill")
 import("RColorBrewer")
 import("BiocParallel")
 
+## import("S4Vectors")
 importClassesFrom("S4Vectors", "Rle", "DataFrame")
 importFrom("S4Vectors", "split", "Rle", "DataFrame")
+importMethodsFrom("S4Vectors", "as.matrix")
 
 ## Additional imports proposed by R CMD check:
 importFrom("graphics", "abline", "barplot", "close.screen", "hist",
@@ -43,7 +45,7 @@ importMethodsFrom("MSnbase", "intensity", "mz", "rtime", "fileNames", "fromFile"
                   "spectra", "impute", "isCentroided", "polarity", "[", "bin",
                   "clean", "featureNames", "filterAcquisitionNum", "filterMz",
                   "filterRt", "normalize", "pickPeaks", "removePeaks",
-                  "removeReporters", "smooth", "trimMz")
+                  "removeReporters", "smooth", "trimMz", "splitByFile", "[[")
 importFrom("MSnbase", "as.data.frame.Spectrum")
 
 export(
@@ -190,13 +192,19 @@ export(
     "do_detectFeatures_addPredIsoROIs",
     "imputeLinInterpol",
     "useOriginalCode",
-    "setAs"
+    "setAs",
+    "do_groupFeatures_density",
+    "do_groupFeatures_mzClust",
+    "do_groupFeatures_nearest",
+    "do_adjustRtime_featureGroups"
 )
 
 ## New analysis methods
 exportMethods(
     "showError",
-    "detectFeatures"
+    "detectFeatures",
+    "groupFeatures",
+    "adjustRtime"
 )
 
 ## New Param classes
@@ -205,7 +213,12 @@ exportClasses(
     "MatchedFilterParam",
     "MassifquantParam",
     "MSWParam",
-    "CentWavePredIsoParam"
+    "CentWavePredIsoParam",
+    "FeatureDensityParam",
+    "MzClustParam",
+    "NearestFeaturesParam",
+    "FeatureGroupsParam",
+    "ObiwarpParam"
 )
 ## Param methods
 exportMethods(
@@ -294,13 +307,59 @@ exportMethods(
     "mzIntervalExtension<-",
     "polarity",
     "polarity<-",
-    "rtime",
-    "mz",
-    "intensity"
+    ## FeatureDensityParam
+    "sampleGroups",
+    "sampleGroups<-",
+    "bw",
+    "bw<-",
+    "minFraction",
+    "minFraction<-",
+    "minSamples",
+    "minSamples<-",
+    "maxFeatures",
+    "maxFeatures<-",
+    ## MzClustParam
+    "absMz",
+    "absMz<-",
+    ## NearestFeaturesParam
+    "absRt",
+    "absRt<-",
+    "mzVsRtBalance",
+    "mzVsRtBalance<-",
+    "kNN",
+    "kNN<-",
+    "extraFeatures",
+    "extraFeatures<-",
+    "smooth",
+    "smooth<-",
+    "span",
+    "span<-",
+    "family",
+    "family<-",
+    ## ObiwarpParam
+    "centerSample",
+    "centerSample<-",
+    "response",
+    "response<-",
+    "distFun",
+    "distFun<-",
+    "gapInit",
+    "gapInit<-",
+    "gapExtend",
+    "gapExtend<-",
+    "factorDiag",
+    "factorDiag<-",
+    "factorGap",
+    "factorGap<-",
+    "localAlignment",
+    "localAlignment<-",
+    "initPenalty",
+    "initPenalty<-"
 )
 ## Param class functions
 export("CentWaveParam", "MatchedFilterParam", "MassifquantParam", "MSWParam",
-       "CentWavePredIsoParam")
+       "CentWavePredIsoParam", "FeatureDensityParam", "MzClustParam",
+       "NearestFeaturesParam", "FeatureGroupsParam", "ObiwarpParam")
 ## Param class methods.
 
 ## New Classes
@@ -335,5 +394,8 @@ exportMethods("hasDetectedFeatures",
               "dropAdjustedRtime",
               "dropFeatureGroups",
               "dropFeatures",
-              "spectra"
+              "spectra",
+              "rtime",
+              "mz",
+              "intensity"
               )
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -3,10 +3,16 @@
 
 ## A
 setGeneric("absent", function(object, class, minfrac) standardGeneric("absent"))
+setGeneric("absMz", function(object, ...) standardGeneric("absMz"))
+setGeneric("absMz<-", function(object, value) standardGeneric("absMz<-"))
+setGeneric("absRt", function(object, ...) standardGeneric("absRt"))
+setGeneric("absRt<-", function(object, value) standardGeneric("absRt<-"))
 setGeneric("addParams", function(object, ...) standardGeneric("addParams"))
 setGeneric("addParams<-", function(object, value) standardGeneric("addParams<-"))
 setGeneric("addProcessHistory", function(object, ...)
     standardGeneric("addProcessHistory"))
+setGeneric("adjustRtime", function(object, param, ...)
+    standardGeneric("adjustRtime"))
 setGeneric("adjustedRtime", function(object, ...) standardGeneric("adjustedRtime"))
 setGeneric("adjustedRtime<-", function(object, value)
     standardGeneric("adjustedRtime<-"))
@@ -19,11 +25,16 @@ setGeneric("baseValue", function(object, ...) standardGeneric("baseValue"))
 setGeneric("baseValue<-", function(object, value) standardGeneric("baseValue<-"))
 setGeneric("binSize", function(object, ...) standardGeneric("binSize"))
 setGeneric("binSize<-", function(object, value) standardGeneric("binSize<-"))
+setGeneric("bw", function(object) standardGeneric("bw"))
+setGeneric("bw<-", function(object, value) standardGeneric("bw<-"))
 
 ## C
 setGeneric("calibrate", function(object, ...) standardGeneric("calibrate"))
 setGeneric("checkBack", function(object, ...) standardGeneric("checkBack"))
 setGeneric("checkBack<-", function(object, value) standardGeneric("checkBack<-"))
+setGeneric("centerSample", function(object) standardGeneric("centerSample"))
+setGeneric("centerSample<-", function(object, value)
+    standardGeneric("centerSample<-"))
 setGeneric("collect", function(object, ...) standardGeneric("collect"))
 setGeneric("consecMissedLimit", function(object, ...)
     standardGeneric("consecMissedLimit"))
@@ -41,14 +52,28 @@ setGeneric("detectFeatures", function(object, param, ...)
 setGeneric("diffreport", function(object, ...) standardGeneric("diffreport"))
 setGeneric("distance", function(object, ...) standardGeneric("distance"))
 setGeneric("distance<-", function(object, value) standardGeneric("distance<-"))
+setGeneric("distFun", function(object) standardGeneric("distFun"))
+setGeneric("distFun<-", function(object, value) standardGeneric("distFun<-"))
 setGeneric("dropAdjustedRtime", function(object, ...)
     standardGeneric("dropAdjustedRtime"))
 setGeneric("dropFeatureGroups", function(object, ...)
     standardGeneric("dropFeatureGroups"))
 setGeneric("dropFeatures", function(object, ...)
     standardGeneric("dropFeatures"))
 
+## E
+setGeneric("extraFeatures", function(object, ...)
+    standardGeneric("extraFeatures"))
+setGeneric("extraFeatures<-", function(object, value)
+    standardGeneric("extraFeatures<-"))
+
 ## F
+setGeneric("factorDiag", function(object) standardGeneric("factorDiag"))
+setGeneric("factorDiag<-", function(object, value) standardGeneric("factorDiag<-"))
+setGeneric("factorGap", function(object) standardGeneric("factorGap"))
+setGeneric("factorGap<-", function(object, value) standardGeneric("factorGap<-"))
+setGeneric("family", function(object, ...) standardGeneric("family"))
+setGeneric("family<-", function(object, value) standardGeneric("family<-"))
 setGeneric("features", function(object, ...) standardGeneric("features"))
 setGeneric("features<-", function(object, value)
     standardGeneric("features<-"))
@@ -96,6 +121,10 @@ setGeneric("fwhm", function(object, ...) standardGeneric("fwhm"))
 setGeneric("fwhm<-", function(object, value) standardGeneric("fwhm<-"))
 
 ## G
+setGeneric("gapExtend", function(object) standardGeneric("gapExtend"))
+setGeneric("gapExtend<-", function(object, value) standardGeneric("gapExtend<-"))
+setGeneric("gapInit", function(object) standardGeneric("gapInit"))
+setGeneric("gapInit<-", function(object, value) standardGeneric("gapInit<-"))
 setGeneric("getEIC", function(object, ...) standardGeneric("getEIC"))
 setGeneric("getMsnScan", function(object, ...) standardGeneric("getMsnScan"))
 setGeneric("getPeaks", function(object, ...) standardGeneric("getPeaks"))
@@ -107,6 +136,8 @@ setGeneric("group.density", function(object, ...) standardGeneric("group.density
 setGeneric("group.mzClust", function(object, ...) standardGeneric("group.mzClust"))
 setGeneric("group.nearest", function(object, ...) standardGeneric("group.nearest"))
 setGeneric("group", function(object, ...) standardGeneric("group"))
+setGeneric("groupFeatures", function(object, param, ...)
+           standardGeneric("groupFeatures"))
 setGeneric("groupidx", function(object) standardGeneric("groupidx"))
 setGeneric("groupidx<-", function(object, value) standardGeneric("groupidx<-"))
 setGeneric("groupnames", function(object, ...) standardGeneric("groupnames"))
@@ -132,10 +163,19 @@ setGeneric("index<-", function(object, value) standardGeneric("index<-"))
 setGeneric("integrate")
 ##setGeneric("integrate", function(object, ...) standardGeneric("integrate"))
 setGeneric("integrate<-", function(object, value) standardGeneric("integrate<-"))
+setGeneric("initPenalty", function(object) standardGeneric("initPenalty"))
+setGeneric("initPenalty<-", function(object, value) standardGeneric("initPenalty<-"))
 setGeneric("isCentroided", function(object, ...) standardGeneric("isCentroided"))
 
+## K
+setGeneric("kNN", function(object, ...) standardGeneric("kNN"))
+setGeneric("kNN<-", function(object, value) standardGeneric("kNN<-"))
+
+
 ## L
 setGeneric("levelplot", function(x, data, ...) standardGeneric("levelplot"))
+setGeneric("localAlignment", function(object) standardGeneric("localAlignment"))
+setGeneric("localAlignment<-", function(object, value) standardGeneric("localAlignment<-"))
 setGeneric("loadRaw", function(object, ...) standardGeneric("loadRaw"))
 
 ## M
@@ -144,12 +184,18 @@ setGeneric("max")
 setGeneric("max<-", function(object, value) standardGeneric("max<-"))
 setGeneric("maxCharge", function(object) standardGeneric("maxCharge"))
 setGeneric("maxCharge<-", function(object, value) standardGeneric("maxCharge<-"))
+setGeneric("maxFeatures", function(object) standardGeneric("maxFeatures"))
+setGeneric("maxFeatures<-", function(object, value) standardGeneric("maxFeatures<-"))
 setGeneric("maxIso", function(object) standardGeneric("maxIso"))
 setGeneric("maxIso<-", function(object, value) standardGeneric("maxIso<-"))
 setGeneric("makeacqNum", function(object, freq, start=1) standardGeneric("makeacqNum"))
+setGeneric("minFraction", function(object) standardGeneric("minFraction"))
+setGeneric("minFraction<-", function(object, value) standardGeneric("minFraction<-"))
 setGeneric("minNoiseLevel", function(object, ...) standardGeneric("minNoiseLevel"))
 setGeneric("minNoiseLevel<-", function(object, value)
     standardGeneric("minNoiseLevel<-"))
+setGeneric("minSamples", function(object) standardGeneric("minSamples"))
+setGeneric("minSamples<-", function(object, value) standardGeneric("minSamples<-"))
 setGeneric("mslevel", function(object, ...) standardGeneric("mslevel"))
 setGeneric("mslevel<-", function(object, value) standardGeneric("mslevel<-"))
 setGeneric("msnparent2ms", function(object, ...) standardGeneric("msnparent2ms"))
@@ -164,6 +210,10 @@ setGeneric("mzIntervalExtension", function(object, ...)
     standardGeneric("mzIntervalExtension"))
 setGeneric("mzIntervalExtension<-", function(object, value)
     standardGeneric("mzIntervalExtension<-"))
+setGeneric("mzVsRtBalance", function(object, ...)
+    standardGeneric("mzVsRtBalance"))
+setGeneric("mzVsRtBalance<-", function(object, value)
+    standardGeneric("mzVsRtBalance<-"))
 
 ## N
 setGeneric("nearbyPeak", function(object, ...) standardGeneric("nearbyPeak"))
@@ -227,6 +277,8 @@ setGeneric("progressInfoUpdate", function(object) standardGeneric("progressInfoU
 setGeneric("rawEIC", function(object, ...) standardGeneric("rawEIC"))
 setGeneric("rawMat", function(object, ...) standardGeneric("rawMat"))
 setGeneric("rawMZ", function(object, ...) standardGeneric("rawMZ"))
+setGeneric("response", function(object) standardGeneric("response"))
+setGeneric("response<-", function(object, value) standardGeneric("response<-"))
 setGeneric("retcor", function(object, ...) standardGeneric("retcor"))
 setGeneric("retcor.peakgroups", function(object, ...) standardGeneric("retcor.peakgroups"))
 setGeneric("retcor.obiwarp", function(object, ...) standardGeneric("retcor.obiwarp"))
@@ -242,22 +294,28 @@ setGeneric("rtrange", function(object) standardGeneric("rtrange"))
 ## S
 setGeneric("sampclass", function(object) standardGeneric("sampclass"))
 setGeneric("sampclass<-", function(object, value) standardGeneric("sampclass<-"))
+setGeneric("sampleGroups", function(object) standardGeneric("sampleGroups"))
+setGeneric("sampleGroups<-", function(object, value)
+    standardGeneric("sampleGroups<-"))
 setGeneric("sampnames", function(object) standardGeneric("sampnames"))
 setGeneric("sampnames<-", function(object, value) standardGeneric("sampnames<-"))
 setGeneric("scales", function(object, ...) standardGeneric("scales"))
 setGeneric("scales<-", function(object, value) standardGeneric("scales<-"))
 setGeneric("scanrange", function(object, ...) standardGeneric("scanrange"))
 setGeneric("scanrange<-", function(object, value) standardGeneric("scanrange<-"))
-setGeneric("sigma")
+setGeneric("sigma", function(object, value) standardGeneric("sigma"))
 setGeneric("sigma<-", function(object, value) standardGeneric("sigma<-"))
 setGeneric("showError", function(object, ...) standardGeneric("showError"))
+setGeneric("smooth<-", function(object, value) standardGeneric("smooth<-"))
 setGeneric("snthresh", function(object, ...) standardGeneric("snthresh"))
 setGeneric("snthresh<-", function(object, value) standardGeneric("snthresh<-"))
 setGeneric("snthreshIsoROIs", function(object, ...)
     standardGeneric("snthreshIsoROIs"))
 setGeneric("snthreshIsoROIs<-", function(object, value)
     standardGeneric("snthreshIsoROIs<-"))
 setGeneric("sortMz", function(object, ...) standardGeneric("sortMz"))
+setGeneric("span", function(object, ...) standardGeneric("span"))
+setGeneric("span<-", function(object, value) standardGeneric("span<-"))
 setGeneric("specDist", function(object, ...) standardGeneric("specDist"))
 setGeneric("specDist.meanMZmatch",
            function(peakTable1, peakTable2, matchdist=1, matchrate=1,