# Wavelet-Based Models for Tiling Array Transcriptome Analysis

## Documentation for package ‘waveTiling’ version 1.18.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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"