Wavelet-Based Models for Tiling Array Transcriptome Analysis

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Documentation for package ‘waveTiling’ version 1.22.0

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A B C F G I M P S W

-- A --

addPheno Add phenotypic info to 'WaveTilingFeatureSet'
addPheno-method Class "WaveTilingFeatureSet"

-- B --

bgCorrQn Background correction and quantile normalization
bgCorrQn-method Class "WaveTilingFeatureSet"

-- C --

cel2TilingFeatureSet Read CEL-files to TilingFeatureSet

-- F --

filterOverlap function to filter probe sequence overlaps and remap probes
filterOverlap-method Class "WaveTilingFeatureSet"

-- G --

GenomeInfo Class "genomeInfo"
GenomeInfo-class Class "genomeInfo"
getAlpha Class "WfmInf"
getAlpha-method Class "WfmInf"
getBetaWav Class "WfmFit"
getBetaWav-method Class "WfmFit"
getChromosome Class "MapFilterProbe"
getChromosome-method Class "MapFilterProbe"
getChromosome-method Class "WfmFit"
getDataOrigSpace Class "WfmFit"
getDataOrigSpace-method Class "WfmFit"
getDataWaveletSpace Class "WfmFit"
getDataWaveletSpace-method Class "WfmFit"
getDelta Class "WfmInf"
getDelta-method Class "WfmInf"
getDesignMatrix Class "WfmFit"
getDesignMatrix-method Class "WfmFit"
getEff Class "WfmInf"
getEff-method Class "WfmInf"
getF Class "WfmFit"
getF-method Class "WfmFit"
getFDR Class "WfmInf"
getFDR-method Class "WfmInf"
getFilteredIndices Class "MapFilterProbe"
getFilteredIndices-method Class "MapFilterProbe"
getGenomeInfo Class "WfmFit"
getGenomeInfo-method Class "WfmFit"
getGenomeInfo-method Class "WfmInf"
getGenomicRegions Class "WfmInf"
getGenomicRegions-method Class "WfmInf"
getGroupNames Class "WaveTilingFeatureSet"
getGroupNames-method Class "WaveTilingFeatureSet"
getKj Class "WfmFit"
getKj-method Class "WfmFit"
getMaxPos Class "WfmFit"
getMaxPos-method Class "WfmFit"
getMinPos Class "WfmFit"
getMinPos-method Class "WfmFit"
getNoGroups Class "WaveTilingFeatureSet"
getNoGroups-method Class "WaveTilingFeatureSet"
getNoLevels Class "WfmFit"
getNoLevels-method Class "WfmFit"
getNonAnnotatedRegions Get non-annotated regions
getNonAnnotatedRegions-method Class "WfmInf"
getNoProbes Class "WfmFit"
getNoProbes-method Class "WfmFit"
getPhenoInfo Class "WfmFit"
getPhenoInfo-method Class "WfmFit"
getPosition Class "MapFilterProbe"
getPosition-method Class "MapFilterProbe"
getPrior Class "WfmFit"
getPrior-method Class "WfmFit"
getProbePosition Class "WfmFit"
getProbePosition-method Class "WfmFit"
getRegions Class "WfmInf"
getRegions-method Class "WfmInf"
getReplics Class "WaveTilingFeatureSet"
getReplics-method Class "WaveTilingFeatureSet"
getSigGenes Get significant genes
getSigGenes-method Class "WfmInf"
getSigProbes Class "WfmInf"
getSigProbes-method Class "WfmInf"
getSmoothPar Class "WfmFit"
getSmoothPar-method Class "WfmFit"
getStrand Class "MapFilterProbe"
getStrand-method Class "MapFilterProbe"
getStrand-method Class "WfmFit"
getTwoSided Class "WfmInf"
getTwoSided-method Class "WfmInf"
getVarBetaWav Class "WfmFit"
getVarBetaWav-method Class "WfmFit"
getVarEff Class "WfmInf"
getVarEff-method Class "WfmInf"
getVarEps Class "WfmFit"
getVarEps-method Class "WfmFit"
getVarF Class "WfmFit"
getVarF-method Class "WfmFit"
getWaveletFilter Class "WfmFit"
getWaveletFilter-method Class "WfmFit"

-- I --

initialize-method Class "genomeInfo"
initialize-method Class "MapFilterProbe"
initialize-method Class "WaveTilingFeatureSet"
initialize-method Class "WfmFit"
initialize-method Class "WfmFitCircadian"
initialize-method Class "WfmFitCustom"
initialize-method Class "WfmFitFactor"
initialize-method Class "WfmFitTime"
initialize-method Class "WfmInf"
initialize-method Class "WfmInfCompare"
initialize-method Class "WfmInfCustom"
initialize-method Class "WfmInfEffects"
initialize-method Class "WfmInfMeans"
initialize-method Class "WfmInfOverallMean"

-- M --

makeContrasts Construct contrast matrix
makeDesign Construct design matrix
MapFilterProbe Class "MapFilterProbe"
MapFilterProbe-class Class "MapFilterProbe"

-- P --

plotWfm plot model fit and genomic regions
plotWfm-method Class "WfmInf"

-- S --

selectProbesFromFilterOverlap select probes from 'MapFilterProbe' object
selectProbesFromFilterOverlap-method Class "MapFilterProbe"
selectProbesFromTilingFeatureSet select probes from 'WaveTilingFeatureSet' object
selectProbesFromTilingFeatureSet-method Class "WaveTilingFeatureSet"
show-method Class "genomeInfo"
show-method Class "MapFilterProbe"
show-method Class "WaveTilingFeatureSet"
show-method Class "WfmFit"
show-method Class "WfmFitCircadian"
show-method Class "WfmFitCustom"
show-method Class "WfmFitFactor"
show-method Class "WfmFitTime"
show-method Class "WfmInf"
show-method Class "WfmInfCompare"
show-method Class "WfmInfCustom"
show-method Class "WfmInfEffects"
show-method Class "WfmInfMeans"
show-method Class "WfmInfOverallMean"

-- W --

WaveTilingFeatureSet Class "WaveTilingFeatureSet"
WaveTilingFeatureSet-class Class "WaveTilingFeatureSet"
wfm.fit Fit Wfm model to trancriptome data
wfm.fit-method Class "WaveTilingFeatureSet"
wfm.inference Perform transcriptome analysis on fitted wavelet-based functional model
wfm.inference-method Class "WfmFit"
WfmFit Class "WfmFit"
WfmFit-class Class "WfmFit"
WfmFitCircadian Class "WfmFitCircadian"
WfmFitCircadian-class Class "WfmFitCircadian"
WfmFitCustom Class "WfmFitCustom"
WfmFitCustom-class Class "WfmFitCustom"
WfmFitFactor Class "WfmFitFactor"
WfmFitFactor-class Class "WfmFitFactor"
WfmFitTime Class "WfmFitTime"
WfmFitTime-class Class "WfmFitTime"
WfmInf Class "WfmInf"
WfmInf-class Class "WfmInf"
WfmInfCompare Class "WfmInfCompare"
WfmInfCompare-class Class "WfmInfCompare"
WfmInfCustom Class "WfmInfCustom"
WfmInfCustom-class Class "WfmInfCustom"
WfmInfEffects Class "WfmInfEffects"
WfmInfEffects-class Class "WfmInfEffects"
WfmInfMeans Class "WfmInfMeans"
WfmInfMeans-class Class "WfmInfMeans"
WfmInfOverallMean Class "WfmInfOverallMean"
WfmInfOverallMean-class Class "WfmInfOverallMean"