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waveTiling (version 1.14.0)

Wavelet-Based Models for Tiling Array Transcriptome Analysis

Description

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

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Version

Version

1.14.0

License

GPL (>=2)

Maintainer

Kristof De Beuf

Last Published

February 15th, 2017

Functions in waveTiling (1.14.0)

cel2TilingFeatureSet

Read CEL-files to TilingFeatureSet
GenomeInfo-class

Class "genomeInfo"
bgCorrQn

Background correction and quantile normalization
wfm.fit

Fit Wfm model to trancriptome data
WfmInfOverallMean-class

Class "WfmInfOverallMean"
getNonAnnotatedRegions

Get non-annotated regions
getSigGenes

Get significant genes
filterOverlap

function to filter probe sequence overlaps and remap probes
MapFilterProbe-class

Class "MapFilterProbe"
WfmFitFactor-class

Class "WfmFitFactor"
plotWfm

plot model fit and genomic regions
WaveTilingFeatureSet-class

Class "WaveTilingFeatureSet"
wfm.inference

Perform transcriptome analysis on fitted wavelet-based functional model
WfmInf-class

Class "WfmInf"
makeContrasts

Construct contrast matrix
WfmFitTime-class

Class "WfmFitTime"
makeDesign

Construct design matrix
selectProbesFromFilterOverlap

select probes from MapFilterProbe object
WfmInfMeans-class

Class "WfmInfMeans"
addPheno

Add phenotypic info to WaveTilingFeatureSet
WfmInfCompare-class

Class "WfmInfCompare"
WfmInfEffects-class

Class "WfmInfEffects"
WfmInfCustom-class

Class "WfmInfCustom"
selectProbesFromTilingFeatureSet

select probes from WaveTilingFeatureSet object
WfmFitCircadian-class

Class "WfmFitCircadian"
WfmFit-class

Class "WfmFit"
WfmFitCustom-class

Class "WfmFitCustom"