# DNA methylation data analysis and visualization

## Documentation for package ‘methyAnalysis’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

annotateDMRInfo | Annotate the DMR (Differentially Methylated Region)
annotateGRanges | Annotate a GRanges object
asBigMatrix | convert the data matrix in the assayData of a GenoSet as BigMatrix
asBigMatrix-method | convert the data matrix in the assayData of a GenoSet as BigMatrix
asBigMatrix-methods | convert the data matrix in the assayData of a GenoSet as BigMatrix
buildAnnotationTracks | Build annotation tracks for visualizing using Gviz package
checkChrName | check chromosome names
class:MethyGenoSet | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
coerce-method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
combine-method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
createTranscriptTrack | Create a transcript annotation track
detectDMR.slideWin | Detect DMR (Differentially Methylated Region) using slide window smoothing
detection-method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
detection<--method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
estimateCMR.methylation | Estimate the averaged methylation levels within a chromosome region or transcript promoter
estimateMethySeq | Estimate the methylation level (Beta-value) of Methyl-Seq data
exampleMethyGenoSet | Example MethyGenoSet dataset
export.DMRInfo | Output the DMR (Differentially Methylated Region) data information
export.methyGenoSet | Export a MethyGenoSet object to be visualized using external genome browser tools
exprs-method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
exprs<--method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
filterBisulfiteVariant | filtering the variant calls of Bisulfite converted sequencing data
getContinuousRegion | Get continuous chromosome region by merging nearby or overlapping regions
getCoverage | get the coverage based on a given GRanges object
getHistory-method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
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)
initialize-method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
MethyGenoSet | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
MethyGenoSet-class | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
methylated-method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
methylated<--method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
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 the left of the plot
smoothMethyData | Smooth the methylation data
unmethylated-method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
unmethylated<--method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
updateMethyGenoSet | Update old version MethyGenoSet objects
[-method | Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class