waveTiling: Wavelet-Based Models for Tiling Array Transcriptome Analysis
Version 1.18.0

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

Browse man pages Browse package API and functions Browse package files

AuthorKristof De Beuf <kristof.debeuf@UGent.be>, Peter Pipelers <peter.pipelers@ugent.be> and Lieven Clement <lieven.clement@gmail.com>
Bioconductor views DifferentialExpression GeneExpression Microarray TimeCourse
Date of publicationNone
MaintainerKristof De Beuf <kristof.debeuf@UGent.be>
LicenseGPL (>=2)
Version1.18.0
URL https://r-forge.r-project.org/projects/wavetiling/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("waveTiling")

Man pages

addPheno: Add phenotypic info to 'WaveTilingFeatureSet'
bgCorrQn: Background correction and quantile normalization
cel2TilingFeatureSet: Read CEL-files to TilingFeatureSet
filterOverlap: function to filter probe sequence overlaps and remap probes
GenomeInfo-class: Class "genomeInfo"
getNonAnnotatedRegions: Get non-annotated regions
getSigGenes: Get significant genes
makeContrasts: Construct contrast matrix
makeDesign: Construct design matrix
MapFilterProbe-class: Class "MapFilterProbe"
plotWfm: plot model fit and genomic regions
selectProbesFromFilterOverlap: select probes from 'MapFilterProbe' object
selectProbesFromTilingFeatureSet: select probes from 'WaveTilingFeatureSet' object
WaveTilingFeatureSet-class: Class "WaveTilingFeatureSet"
wfm.fit: Fit Wfm model to trancriptome data
WfmFitCircadian-class: Class "WfmFitCircadian"
WfmFit-class: Class "WfmFit"
WfmFitCustom-class: Class "WfmFitCustom"
WfmFitFactor-class: Class "WfmFitFactor"
WfmFitTime-class: Class "WfmFitTime"
WfmInf-class: Class "WfmInf"
WfmInfCompare-class: Class "WfmInfCompare"
WfmInfCustom-class: Class "WfmInfCustom"
WfmInfEffects-class: Class "WfmInfEffects"
wfm.inference: Perform transcriptome analysis on fitted wavelet-based...
WfmInfMeans-class: Class "WfmInfMeans"
WfmInfOverallMean-class: Class "WfmInfOverallMean"

Functions

GenomeInfo Man page
GenomeInfo-class Man page
MapFilterProbe Man page
MapFilterProbe-class Man page
MapMar Source code
MapMarImp Source code
WaveMarEstVarJ Source code
WaveTilingFeatureSet Man page
WaveTilingFeatureSet-class Man page
WfmFit Man page
WfmFit-class Man page
WfmFitCircadian Man page
WfmFitCircadian-class Man page
WfmFitCustom Man page
WfmFitCustom-class Man page
WfmFitFactor Man page
WfmFitFactor-class Man page
WfmFitTime Man page
WfmFitTime-class 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
WfmInfMeans Man page
WfmInfMeans-class Man page
WfmInfOverallMean Man page
WfmInfOverallMean-class Man page
addPheno Man page
addPheno,WaveTilingFeatureSet-method Man page
bgCorrQn Man page
bgCorrQn,WaveTilingFeatureSet-method Man page
cel2TilingFeatureSet Man page Source code
extractChrFromFasta Source code
filterOverlap Man page
filterOverlap,WaveTilingFeatureSet-method 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
getF,WfmFit-method Man page
getFDR Man page
getFDR,WfmInf-method Man page
getFilteredIndices Man page
getFilteredIndices,MapFilterProbe-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
getNoProbes Man page
getNoProbes,WfmFit-method Man page
getNonAnnotatedRegions Man page
getNonAnnotatedRegions,WfmFit,WfmInf-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,WfmFit-method Man page
initialize,WfmFitCircadian-method Man page
initialize,WfmFitCustom-method Man page
initialize,WfmFitFactor-method Man page
initialize,WfmFitTime-method Man page
initialize,WfmInf-method Man page
initialize,WfmInfCompare-method Man page
initialize,WfmInfCustom-method Man page
initialize,WfmInfEffects-method Man page
initialize,WfmInfMeans-method Man page
initialize,WfmInfOverallMean-method Man page
makeContrasts Man page Source code
makeDesign Man page Source code
makeNewAnnotationTextOverlay Source code
makeNewAnnotationTrack Source code
makeNewTranscriptRectangleOverlay Source code
normVec Source code
plotWfm Man page
plotWfm,WfmFit,WfmInf-method Man page
pm2mm Source code
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,WfmFit-method Man page
show,WfmFitCircadian-method Man page
show,WfmFitCustom-method Man page
show,WfmFitFactor-method Man page
show,WfmFitTime-method Man page
show,WfmInf-method Man page
show,WfmInfCompare-method Man page
show,WfmInfCustom-method Man page
show,WfmInfEffects-method Man page
show,WfmInfMeans-method Man page
show,WfmInfOverallMean-method Man page
wave.backtransform Source code
wave.backtransformK Source code
wave.transform Source code
wfm.fit Man page
wfm.fit,WaveTilingFeatureSet-method Man page
wfm.inference Man page
wfm.inference,WfmFit-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/allClasses.R
R/allGenerics.R
R/helperFunctions.R
R/initialize-methods.R
R/methods-MapFilterProbe.R
R/methods-WaveTilingFeatureSet.R
R/methods-WfmFit.R
R/methods-WfmInf.R
R/show-methods.R
build
build/vignette.rds
inst
inst/NEWS.Rd
inst/doc
inst/doc/waveTiling-vignette.R
inst/doc/waveTiling-vignette.Rnw
inst/doc/waveTiling-vignette.pdf
man
man/GenomeInfo-class.Rd
man/MapFilterProbe-class.Rd
man/WaveTilingFeatureSet-class.Rd
man/WfmFit-class.Rd
man/WfmFitCircadian-class.Rd
man/WfmFitCustom-class.Rd
man/WfmFitFactor-class.Rd
man/WfmFitTime-class.Rd
man/WfmInf-class.Rd
man/WfmInfCompare-class.Rd
man/WfmInfCustom-class.Rd
man/WfmInfEffects-class.Rd
man/WfmInfMeans-class.Rd
man/WfmInfOverallMean-class.Rd
man/addPheno.Rd
man/bgCorrQn.Rd
man/cel2TilingFeatureSet.Rd
man/filterOverlap.Rd
man/getNonAnnotatedRegions.Rd
man/getSigGenes.Rd
man/makeContrasts.Rd
man/makeDesign.Rd
man/plotWfm.Rd
man/selectProbesFromFilterOverlap.Rd
man/selectProbesFromTilingFeatureSet.Rd
man/wfm.fit.Rd
man/wfm.inference.Rd
src
src/waveTiling.c
vignettes
vignettes/waveTiling-vignette.Rnw
waveTiling documentation built on May 20, 2017, 9:59 p.m.