addPheno | Add phenotypic info to 'WaveTilingFeatureSet' |
addPheno-method | Class "WaveTilingFeatureSet" |
bgCorrQn | Background correction and quantile normalization |
bgCorrQn-method | Class "WaveTilingFeatureSet" |
cel2TilingFeatureSet | Read CEL-files to TilingFeatureSet |
filterOverlap | function to filter probe sequence overlaps and remap probes |
filterOverlap-method | Class "WaveTilingFeatureSet" |
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" |
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" |
makeContrasts | Construct contrast matrix |
makeDesign | Construct design matrix |
MapFilterProbe | Class "MapFilterProbe" |
MapFilterProbe-class | Class "MapFilterProbe" |
plotWfm | plot model fit and genomic regions |
plotWfm-method | Class "WfmInf" |
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" |
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" |