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NAMESPACE
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NAMESPACE
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import(xcms, commandr)
## IRanges)
importClassesFrom(Biobase, ExpressionSet, AnnotatedDataFrame)
importFrom(Biobase, copyEnv)
importMethodsFrom(IRanges, Rle, runValue, width, Views, viewSums,
findOverlaps)
importFrom(IRanges, PartitioningByEnd, IRanges)
## just for now
## exportPattern("^[^\\.]")
## main data structures
exportClasses("cpExperiment", "cpPeaks", "cpSample")
## stuff from commandr
export(explore, perform, pipeline)
exportMethods(loadSample, genProfile, loadExperiment,
findPeaks, findComps, groupComps, rtcor,
fillPeaks, normalize, summarize, removeBaseline)
## stuff from xcms
export(findPeaks, findPeaks.pipeline)
##
export(LoadPeaksPipeline)
## pipeline stuff
exportClasses("PipelineORlanguage", "ProtoFillPeaks",
"ProtoFillPeaksExtract", "ProtoFindComps",
"ProtoFindCompsSigma", "ProtoFindPeaks",
"ProtoFindPeaksCentWave", "ProtoFindPeaksGauss",
"ProtoFindPeaksMatchedFilter",
"ProtoFindPeaksPipeline", "ProtoGenProfile",
"ProtoGenProfileIntbin", "ProtoGroupComps",
"ProtoGroupCompsAngle", "ProtoGroupCompsDensity",
"ProtoIdentifyCompounds", "ProtoLoadExperiment",
"ProtoLoadExperimentXcms", "ProtoLoadSample",
"ProtoLoadSampleXcms", "ProtoNormalize",
"ProtoNormalizeScale", "ProtoRemoveBaseline",
"ProtoRemoveBaselineMedian", "ProtoRemoveBaselineRbe",
"ProtoRtcor", "ProtoRtcorRloess", "ProtoRtcorSmooth",
"ProtoSummarize", "ProtoSummarizeCommon",
"StageFillPeaks", "StageFindComps", "StageFindPeaks",
"StageGenProfile", "StageGroupComps",
"StageIdentifyCompounds", "StageLoadExperiment",
"StageLoadSample", "StageNormalize",
"StageRemoveBaseline", "StageRtcor", "StageSummarize",
"characterORlanguage", "data.frameORNULL",
"data.frameORNULLORlanguage", "logicalORlanguage",
"numericORlanguage", "ProtoFindPeaksParabola")