DNA methylation data analysis and visualization


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Documentation for package ‘methyAnalysis’ version 1.0.0

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annotateDMRInfo Annotate the DMR (Differentially Methylated Region)
annotateGRanges Annotate a GRanges object
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
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
getContinuousRegion Get continuous chromosome region by merging nearby or overlapping regions
getHistory-method Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
heatmapByChromosome heatmap with chromosome location as x axis
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
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
[-method Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class