methyAnalysis: DNA methylation data analysis and visualization

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.

AuthorPan Du, Richard Bourgon
Date of publicationNone
MaintainerPan Du <dupan.mail@gmail.com>, Lei Huang <lhuang@bsd.uchicago.edu>, Gang Feng <g-feng@northwestern.edu>
LicenseArtistic-2.0
Version1.16.1

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

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