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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("methyAnalysis")
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
Version1.16.1

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

Functions

annotateDMRInfo Man page
annotateGRanges Man page
asBigMatrix Man page
asBigMatrix,GenoSet-method Man page
asBigMatrix-methods Man page
buildAnnotationTracks Man page
checkChrName Man page
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
detectDMR.slideWin Man page
detection<-,MethyGenoSet,ANY-method Man page
detection<-,MethyGenoSet-method Man page
detection,MethyGenoSet-method Man page
estimateCMR.methylation Man page
estimateMethySeq Man page
exampleMethyGenoSet Man page
export.DMRInfo Man page
export.methyGenoSet Man page
exprs<-,MethyGenoSet,ANY-method Man page
exprs<-,MethyGenoSet-method Man page
exprs,MethyGenoSet-method Man page
filterBisulfiteVariant Man page
getContinuousRegion Man page
getCoverage Man page
getHistory,MethyGenoSet-method Man page
heatmapByChromosome Man page
identifyCpG Man page
identifySigDMR Man page
initialize,MethyGenoSet-method Man page
MethyGenoSet Man page
[,MethyGenoSet,ANY,ANY,ANY-method Man page
MethyGenoSet-class Man page
[,MethyGenoSet-method Man page
methylated<-,MethyGenoSet,ANY-method Man page
methylated<-,MethyGenoSet-method Man page
methylated,MethyGenoSet-method Man page
MethyLumiM2GenoSet Man page
plotHeatmapByGene Man page
plotMethylationHeatmapByGene Man page
plotTracksWithDataTrackInfo Man page
smoothMethyData Man page
unmethylated<-,MethyGenoSet,ANY-method Man page
unmethylated<-,MethyGenoSet-method Man page
unmethylated,MethyGenoSet-method Man page
updateMethyGenoSet Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.