waveTiling: Wavelet-Based Models for Tiling Array Transcriptome Analysis

This package is designed to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.

AuthorKristof De Beuf <kristof.debeuf@UGent.be>, Peter Pipelers <peter.pipelers@ugent.be> and Lieven Clement <lieven.clement@gmail.com>
Date of publicationNone
MaintainerKristof De Beuf <kristof.debeuf@UGent.be>
LicenseGPL (>=2)
Version1.16.0
https://r-forge.r-project.org/projects/wavetiling/

View on Bioconductor

Functions

addPheno Man page
addPheno,WaveTilingFeatureSet-method Man page
bgCorrQn Man page
bgCorrQn,WaveTilingFeatureSet-method Man page
cel2TilingFeatureSet Man page
filterOverlap Man page
filterOverlap,WaveTilingFeatureSet-method Man page
GenomeInfo Man page
GenomeInfo-class Man page
getAlpha Man page
getAlpha,WfmInf-method Man page
getBetaWav Man page
getBetaWav,WfmFit-method Man page
getChromosome Man page
getChromosome,MapFilterProbe-method Man page
getChromosome,WfmFit-method Man page
getDataOrigSpace Man page
getDataOrigSpace,WfmFit-method Man page
getDataWaveletSpace Man page
getDataWaveletSpace,WfmFit-method Man page
getDelta Man page
getDelta,WfmInf-method Man page
getDesignMatrix Man page
getDesignMatrix,WfmFit-method Man page
getEff Man page
getEff,WfmInf-method Man page
getF Man page
getFDR Man page
getFDR,WfmInf-method Man page
getFilteredIndices Man page
getFilteredIndices,MapFilterProbe-method Man page
getF,WfmFit-method Man page
getGenomeInfo Man page
getGenomeInfo,WfmFit-method Man page
getGenomeInfo,WfmInf-method Man page
getGenomicRegions Man page
getGenomicRegions,WfmInf-method Man page
getGroupNames Man page
getGroupNames,WaveTilingFeatureSet-method Man page
getKj Man page
getKj,WfmFit-method Man page
getMaxPos Man page
getMaxPos,WfmFit-method Man page
getMinPos Man page
getMinPos,WfmFit-method Man page
getNoGroups Man page
getNoGroups,WaveTilingFeatureSet-method Man page
getNoLevels Man page
getNoLevels,WfmFit-method Man page
getNonAnnotatedRegions Man page
getNonAnnotatedRegions,WfmFit,WfmInf-method Man page
getNoProbes Man page
getNoProbes,WfmFit-method Man page
getPhenoInfo Man page
getPhenoInfo,WfmFit-method Man page
getPosition Man page
getPosition,MapFilterProbe-method Man page
getPrior Man page
getPrior,WfmFit-method Man page
getProbePosition Man page
getProbePosition,WfmFit-method Man page
getRegions Man page
getRegions,WfmInf-method Man page
getReplics Man page
getReplics,WaveTilingFeatureSet-method Man page
getSigGenes Man page
getSigGenes,WfmFit,WfmInf-method Man page
getSigProbes Man page
getSigProbes,WfmInf-method Man page
getSmoothPar Man page
getSmoothPar,WfmFit-method Man page
getStrand Man page
getStrand,MapFilterProbe-method Man page
getStrand,WfmFit-method Man page
getTwoSided Man page
getTwoSided,WfmInf-method Man page
getVarBetaWav Man page
getVarBetaWav,WfmFit-method Man page
getVarEff Man page
getVarEff,WfmInf-method Man page
getVarEps Man page
getVarEps,WfmFit-method Man page
getVarF Man page
getVarF,WfmFit-method Man page
getWaveletFilter Man page
getWaveletFilter,WfmFit-method Man page
initialize,GenomeInfo-method Man page
initialize,MapFilterProbe-method Man page
initialize,WaveTilingFeatureSet-method Man page
initialize,WfmFitCircadian-method Man page
initialize,WfmFitCustom-method Man page
initialize,WfmFitFactor-method Man page
initialize,WfmFit-method Man page
initialize,WfmFitTime-method Man page
initialize,WfmInfCompare-method Man page
initialize,WfmInfCustom-method Man page
initialize,WfmInfEffects-method Man page
initialize,WfmInfMeans-method Man page
initialize,WfmInf-method Man page
initialize,WfmInfOverallMean-method Man page
makeContrasts Man page
makeDesign Man page
MapFilterProbe Man page
MapFilterProbe-class Man page
plotWfm Man page
plotWfm,WfmFit,WfmInf-method Man page
pmStrand,WaveTilingFeatureSet-method Man page
selectProbesFromFilterOverlap Man page
selectProbesFromFilterOverlap,MapFilterProbe-method Man page
selectProbesFromTilingFeatureSet Man page
selectProbesFromTilingFeatureSet,WaveTilingFeatureSet-method Man page
show,GenomeInfo-method Man page
show,MapFilterProbe-method Man page
show,WaveTilingFeatureSet-method Man page
show,WfmFitCircadian-method Man page
show,WfmFitCustom-method Man page
show,WfmFitFactor-method Man page
show,WfmFit-method Man page
show,WfmFitTime-method Man page
show,WfmInfCompare-method Man page
show,WfmInfCustom-method Man page
show,WfmInfEffects-method Man page
show,WfmInfMeans-method Man page
show,WfmInf-method Man page
show,WfmInfOverallMean-method Man page
WaveTilingFeatureSet Man page
WaveTilingFeatureSet-class Man page
wfm.fit Man page
WfmFit Man page
WfmFitCircadian Man page
WfmFitCircadian-class Man page
WfmFit-class Man page
WfmFitCustom Man page
WfmFitCustom-class Man page
WfmFitFactor Man page
WfmFitFactor-class Man page
WfmFitTime Man page
WfmFitTime-class Man page
wfm.fit,WaveTilingFeatureSet-method Man page
WfmInf Man page
WfmInf-class Man page
WfmInfCompare Man page
WfmInfCompare-class Man page
WfmInfCustom Man page
WfmInfCustom-class Man page
WfmInfEffects Man page
WfmInfEffects-class Man page
wfm.inference Man page
wfm.inference,WfmFit-method Man page
WfmInfMeans Man page
WfmInfMeans-class Man page
WfmInfOverallMean Man page
WfmInfOverallMean-class Man page

Files

waveTiling/DESCRIPTION
waveTiling/NAMESPACE
waveTiling/R
waveTiling/R/allClasses.R waveTiling/R/allGenerics.R waveTiling/R/helperFunctions.R waveTiling/R/initialize-methods.R waveTiling/R/methods-MapFilterProbe.R waveTiling/R/methods-WaveTilingFeatureSet.R waveTiling/R/methods-WfmFit.R waveTiling/R/methods-WfmInf.R waveTiling/R/show-methods.R
waveTiling/build
waveTiling/build/vignette.rds
waveTiling/inst
waveTiling/inst/NEWS.Rd
waveTiling/inst/doc
waveTiling/inst/doc/waveTiling-vignette.R
waveTiling/inst/doc/waveTiling-vignette.Rnw
waveTiling/inst/doc/waveTiling-vignette.pdf
waveTiling/man
waveTiling/man/GenomeInfo-class.Rd waveTiling/man/MapFilterProbe-class.Rd waveTiling/man/WaveTilingFeatureSet-class.Rd waveTiling/man/WfmFit-class.Rd waveTiling/man/WfmFitCircadian-class.Rd waveTiling/man/WfmFitCustom-class.Rd waveTiling/man/WfmFitFactor-class.Rd waveTiling/man/WfmFitTime-class.Rd waveTiling/man/WfmInf-class.Rd waveTiling/man/WfmInfCompare-class.Rd waveTiling/man/WfmInfCustom-class.Rd waveTiling/man/WfmInfEffects-class.Rd waveTiling/man/WfmInfMeans-class.Rd waveTiling/man/WfmInfOverallMean-class.Rd waveTiling/man/addPheno.Rd waveTiling/man/bgCorrQn.Rd waveTiling/man/cel2TilingFeatureSet.Rd waveTiling/man/filterOverlap.Rd waveTiling/man/getNonAnnotatedRegions.Rd waveTiling/man/getSigGenes.Rd waveTiling/man/makeContrasts.Rd waveTiling/man/makeDesign.Rd waveTiling/man/plotWfm.Rd waveTiling/man/selectProbesFromFilterOverlap.Rd waveTiling/man/selectProbesFromTilingFeatureSet.Rd waveTiling/man/wfm.fit.Rd waveTiling/man/wfm.inference.Rd
waveTiling/src
waveTiling/src/waveTiling.c
waveTiling/vignettes
waveTiling/vignettes/waveTiling-vignette.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.