methyAnalysis: DNA methylation data analysis and visualization

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The methyAnalysis package aims for the DNA methylation data analysis and visualization. A MethyGenoSet class is defined to keep the chromosome location information together with the data. The package also includes functions of estimating the methylation levels from Methy-Seq data.

Author
Pan Du, Richard Bourgon
Date of publication
None
Maintainer
Pan Du <dupan.mail@gmail.com>
License
Artistic-2.0
Version
1.16.0

View on Bioconductor

Man pages

annotateDMRInfo
Annotate the DMR (Differentially Methylated Region)
annotateGRanges
Annotate a GRanges object
asBigMatrix-methods
convert the data matrix in the assayData of a GenoSet as...
buildAnnotationTracks
Build annotation tracks for visualizing using Gviz package
checkChrName
check chromosome names
createTranscriptTrack
Create a transcript annotation track
detectDMR.slideWin
Detect DMR (Differentially Methylated Region) using slide...
estimateCMR.methylation
Estimate the averaged methylation levels within a chromosome...
estimateMethySeq
Estimate the methylation level (Beta-value) of Methyl-Seq...
exampleMethyGenoSet
Example MethyGenoSet dataset
export.DMRInfo
Output the DMR (Differentially Methylated Region) data...
export.methyGenoSet
Export a MethyGenoSet object to be visualized using external...
filterBisulfiteVariant
filtering the variant calls of Bisulfite converted sequencing...
getContinuousRegion
Get continuous chromosome region by merging nearby or...
getCoverage
get the coverage based on a given GRanges object
heatmapByChromosome
heatmap with chromosome location as x axis
identifyCpG
Identify the CpG-site locations from a genome library
identifySigDMR
Identify significantly DMR (Differentially Methylated Region)
MethyGenoSet-class
Class MethyGenoSet: contain and describe Illumina Infinium...
MethyLumiM2GenoSet
Coerce objects of MethyLumiM-class to MethyGenoSet
plotHeatmapByGene
plot methylation heatmap by genes
plotMethylationHeatmapByGene
plot methylation heatmap by genes
plotTracksWithDataTrackInfo
plot Tracks with additional DataTrack information added to...
smoothMethyData
Smooth the methylation data
updateMethyGenoSet
Update old version MethyGenoSet objects

Files in this package

methyAnalysis/DESCRIPTION
methyAnalysis/NAMESPACE
methyAnalysis/R
methyAnalysis/R/MethyGenoSet-class.R
methyAnalysis/R/heatmapByChromosome.R
methyAnalysis/R/methyAnalysis.R
methyAnalysis/R/methyl-seq.R
methyAnalysis/build
methyAnalysis/build/vignette.rds
methyAnalysis/data
methyAnalysis/data/exampleMethyGenoSet.rda
methyAnalysis/inst
methyAnalysis/inst/NEWS
methyAnalysis/inst/doc
methyAnalysis/inst/doc/methyAnalysis.R
methyAnalysis/inst/doc/methyAnalysis.Rnw
methyAnalysis/inst/doc/methyAnalysis.pdf
methyAnalysis/inst/scripts
methyAnalysis/man
methyAnalysis/man/MethyGenoSet-class.Rd
methyAnalysis/man/MethyLumiM2GenoSet.Rd
methyAnalysis/man/annotateDMRInfo.Rd
methyAnalysis/man/annotateGRanges.Rd
methyAnalysis/man/asBigMatrix-methods.Rd
methyAnalysis/man/buildAnnotationTracks.Rd
methyAnalysis/man/checkChrName.Rd
methyAnalysis/man/createTranscriptTrack.Rd
methyAnalysis/man/detectDMR.slideWin.Rd
methyAnalysis/man/estimateCMR.methylation.Rd
methyAnalysis/man/estimateMethySeq.Rd
methyAnalysis/man/exampleMethyGenoSet.Rd
methyAnalysis/man/export.DMRInfo.Rd
methyAnalysis/man/export.methyGenoSet.Rd
methyAnalysis/man/filterBisulfiteVariant.Rd
methyAnalysis/man/getContinuousRegion.Rd
methyAnalysis/man/getCoverage.Rd
methyAnalysis/man/heatmapByChromosome.Rd
methyAnalysis/man/identifyCpG.Rd
methyAnalysis/man/identifySigDMR.Rd
methyAnalysis/man/plotHeatmapByGene.Rd
methyAnalysis/man/plotMethylationHeatmapByGene.Rd
methyAnalysis/man/plotTracksWithDataTrackInfo.Rd
methyAnalysis/man/smoothMethyData.Rd
methyAnalysis/man/updateMethyGenoSet.Rd
methyAnalysis/vignettes
methyAnalysis/vignettes/correlation_localWindow.png
methyAnalysis/vignettes/methyAnalysis.Rnw