Estimate the averaged methylation levels within a chromosome region or transcript promoter
Smooth the methylation data
Create a transcript annotation track
Detect DMR (Differentially Methylated Region) using slide window smoothing
check chromosome names
Annotate a GRanges object
Estimate the methylation level (Beta-value) of Methyl-Seq data
filtering the variant calls of Bisulfite converted sequencing data
heatmap with chromosome location as x axis
plotMethylationHeatmapByGene
plot methylation heatmap by genes
Identify significantly DMR (Differentially Methylated Region)
Build annotation tracks for visualizing using Gviz package
get the coverage based on a given GRanges object
plot methylation heatmap by genes
Get continuous chromosome region by merging nearby or overlapping regions
Update old version MethyGenoSet objects
plotTracksWithDataTrackInfo
plot Tracks with additional DataTrack information added to the left of the plot
Coerce objects of MethyLumiM-class to MethyGenoSet
Export a MethyGenoSet object to be visualized using external genome browser tools
Identify the CpG-site locations from a genome library
convert the data matrix in the assayData of a GenoSet as BigMatrix
Example MethyGenoSet dataset
Annotate the DMR (Differentially Methylated Region)
Class MethyGenoSet: contain and describe Illumina Infinium methylation data in GenoSet-class
Output the DMR (Differentially Methylated Region) data information