methyAnalysis: DNA methylation data analysis and visualization
Version 1.18.0

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
Bioconductor views DNAMethylation Microarray Visualization
Date of publicationNone
MaintainerPan Du <dupan.mail@gmail.com>, Lei Huang <lhuang@bsd.uchicago.edu>, Gang Feng <g-feng@northwestern.edu>
LicenseArtistic-2.0
Version1.18.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("methyAnalysis")

Popular man pages

annotateDMRInfo: Annotate the DMR (Differentially Methylated Region)
buildAnnotationTracks: Build annotation tracks for visualizing using Gviz package
checkChrName: check chromosome names
heatmapByChromosome: heatmap with chromosome location as x axis
MethyLumiM2GenoSet: Coerce objects of MethyLumiM-class to MethyGenoSet
plotMethylationHeatmapByGene: plot methylation heatmap by genes
smoothMethyData: Smooth the methylation data
See all...

All man pages Function index File listing

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

Functions

MethyGenoSet Man page Source code
MethyGenoSet-class Man page
MethyLumiM2GenoSet Man page Source code
[,MethyGenoSet,ANY,ANY,ANY-method Man page
[,MethyGenoSet-method Man page
annotateDMRInfo Man page Source code
annotateGRanges Man page Source code
asBigMatrix Man page
asBigMatrix,GenoSet-method Man page
asBigMatrix-methods Man page
buildAnnotationTracks Man page Source code
checkChrName Man page Source code
class:MethyGenoSet Man page
coerce,GenoSet,MethyGenoSet-method Man page
coerce,MethyGenoSet,MethyLumiM-method Man page
coerce,MethyLumiM,MethyGenoSet-method Man page
combine,MethyGenoSet,MethyGenoSet-method Man page
createTranscriptTrack Man page Source code
dentifySigProbe Source code
detectDMR.slideWin Man page Source code
detection,MethyGenoSet-method Man page
detection<-,MethyGenoSet,ANY-method Man page
detection<-,MethyGenoSet-method Man page
estimateCMR.methylation Man page Source code
estimateMethySeq Man page Source code
estimateTrackHeight Source code
estimateTxOrder Source code
exampleMethyGenoSet Man page
export.DMRInfo Man page Source code
export.methyGenoSet Man page Source code
exprs,MethyGenoSet-method Man page
exprs<-,MethyGenoSet,ANY-method Man page
exprs<-,MethyGenoSet-method Man page
filterBisulfiteVariant Man page Source code
getContinuousRegion Man page Source code
getCoverage Man page Source code
getCpGIsland.ucsc Source code
getCytoBand.ucsc Source code
getEntrezAnnotation Source code
getHistory,MethyGenoSet-method Man page
getMethyProbeLocation Source code
heatmapByChromosome Man page Source code
identifyCpG Man page Source code
identifySigDMR Man page Source code
initialize,MethyGenoSet-method Man page
methylated,MethyGenoSet-method Man page
methylated<-,MethyGenoSet,ANY-method Man page
methylated<-,MethyGenoSet-method Man page
plotHeatmapByGene Man page Source code
plotMethylationHeatmapByGene Man page Source code
plotTracksWithDataTrackInfo Man page Source code
probe2gene Source code
setupSlidingTests Source code
smoothMethyData Man page Source code
transcriptDb2GeneRegionTrackByGene Source code
unmethylated,MethyGenoSet-method Man page
unmethylated<-,MethyGenoSet,ANY-method Man page
unmethylated<-,MethyGenoSet-method Man page
updateMethyGenoSet Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/MethyGenoSet-class.R
R/heatmapByChromosome.R
R/methyAnalysis.R
R/methyl-seq.R
build
build/vignette.rds
data
data/exampleMethyGenoSet.rda
inst
inst/NEWS
inst/doc
inst/doc/methyAnalysis.R
inst/doc/methyAnalysis.Rnw
inst/doc/methyAnalysis.pdf
inst/scripts
man
man/MethyGenoSet-class.Rd
man/MethyLumiM2GenoSet.Rd
man/annotateDMRInfo.Rd
man/annotateGRanges.Rd
man/asBigMatrix-methods.Rd
man/buildAnnotationTracks.Rd
man/checkChrName.Rd
man/createTranscriptTrack.Rd
man/detectDMR.slideWin.Rd
man/estimateCMR.methylation.Rd
man/estimateMethySeq.Rd
man/exampleMethyGenoSet.Rd
man/export.DMRInfo.Rd
man/export.methyGenoSet.Rd
man/filterBisulfiteVariant.Rd
man/getContinuousRegion.Rd
man/getCoverage.Rd
man/heatmapByChromosome.Rd
man/identifyCpG.Rd
man/identifySigDMR.Rd
man/plotHeatmapByGene.Rd
man/plotMethylationHeatmapByGene.Rd
man/plotTracksWithDataTrackInfo.Rd
man/smoothMethyData.Rd
man/updateMethyGenoSet.Rd
vignettes
vignettes/correlation_localWindow.png
vignettes/methyAnalysis.Rnw
methyAnalysis documentation built on May 20, 2017, 10:28 p.m.