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methyAnalysis (version 1.14.0)

DNA methylation data analysis and visualization

Description

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.

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Version

Version

1.14.0

License

Artistic-2.0

Maintainer

Pan Du

Last Published

February 15th, 2017

Functions in methyAnalysis (1.14.0)

estimateCMR.methylation

Estimate the averaged methylation levels within a chromosome region or transcript promoter
smoothMethyData

Smooth the methylation data
createTranscriptTrack

Create a transcript annotation track
detectDMR.slideWin

Detect DMR (Differentially Methylated Region) using slide window smoothing
checkChrName

check chromosome names
annotateGRanges

Annotate a GRanges object
estimateMethySeq

Estimate the methylation level (Beta-value) of Methyl-Seq data
filterBisulfiteVariant

filtering the variant calls of Bisulfite converted sequencing data
heatmapByChromosome

heatmap with chromosome location as x axis
plotMethylationHeatmapByGene

plot methylation heatmap by genes
identifySigDMR

Identify significantly DMR (Differentially Methylated Region)
buildAnnotationTracks

Build annotation tracks for visualizing using Gviz package
getCoverage

get the coverage based on a given GRanges object
plotHeatmapByGene

plot methylation heatmap by genes
getContinuousRegion

Get continuous chromosome region by merging nearby or overlapping regions
updateMethyGenoSet

Update old version MethyGenoSet objects
plotTracksWithDataTrackInfo

plot Tracks with additional DataTrack information added to the left of the plot
MethyLumiM2GenoSet

Coerce objects of MethyLumiM-class to MethyGenoSet
export.methyGenoSet

Export a MethyGenoSet object to be visualized using external genome browser tools
identifyCpG

Identify the CpG-site locations from a genome library
asBigMatrix-methods

convert the data matrix in the assayData of a GenoSet as BigMatrix
exampleMethyGenoSet

Example MethyGenoSet dataset
annotateDMRInfo

Annotate the DMR (Differentially Methylated Region)
MethyGenoSet-class

Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
export.DMRInfo

Output the DMR (Differentially Methylated Region) data information