waveTiling: Wavelet-Based Models for Tiling Array Transcriptome Analysis

Share:

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

Author
Kristof De Beuf <kristof.debeuf@UGent.be>, Peter Pipelers <peter.pipelers@ugent.be> and Lieven Clement <lieven.clement@gmail.com>
Date of publication
None
Maintainer
Kristof De Beuf <kristof.debeuf@UGent.be>
License
GPL (>=2)
Version
0.99.2
URLs

View on R-Forge

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"

Files in this package

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