DNA methylation data analysis and visualization

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Documentation for package ‘methyAnalysis’ version 1.30.0

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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