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methyAnalysis (version 1.12.2)

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

1.12.2

License

Artistic-2.0

Maintainer

Pan Du

Last Published

February 15th, 2017

Functions in methyAnalysis (1.12.2)

Output the DMR (Differentially Methylated Region) data information

check chromosome names

createTranscriptTrack

Create a transcript annotation track

smoothMethyData

Smooth the methylation data

plotTracksWithDataTrackInfo

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

export.methyGenoSet

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

annotateDMRInfo

Annotate the DMR (Differentially Methylated Region)

annotateGRanges

Annotate a GRanges object

heatmapByChromosome

heatmap with chromosome location as x axis

get the coverage based on a given GRanges object

estimateCMR.methylation

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

detectDMR.slideWin

Detect DMR (Differentially Methylated Region) using slide window smoothing

filterBisulfiteVariant

filtering the variant calls of Bisulfite converted sequencing data

getContinuousRegion

Get continuous chromosome region by merging nearby or overlapping regions

estimateMethySeq

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

MethyGenoSet-class

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

exampleMethyGenoSet

Example MethyGenoSet dataset

MethyLumiM2GenoSet

Coerce objects of MethyLumiM-class to MethyGenoSet

asBigMatrix-methods

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

buildAnnotationTracks

Build annotation tracks for visualizing using Gviz package

Identify the CpG-site locations from a genome library

Identify significantly DMR (Differentially Methylated Region)

plotHeatmapByGene

plot methylation heatmap by genes

plotMethylationHeatmapByGene

plot methylation heatmap by genes