Man pages for methyAnalysis
DNA methylation data analysis and visualization
| annotateDMRInfo | Annotate the DMR (Differentially Methylated Region) |
| annotateGRanges | Annotate a GRanges object |
| asBigMatrix-methods | convert the data matrix in the assayData of a GenoSet as... |
| buildAnnotationTracks | Build annotation tracks for visualizing using Gviz package |
| checkChrName | check chromosome names |
| createTranscriptTrack | Create a transcript annotation track |
| detectDMR.slideWin | Detect DMR (Differentially Methylated Region) using slide... |
| estimateCMR.methylation | Estimate the averaged methylation levels within a chromosome... |
| estimateMethySeq | Estimate the methylation level (Beta-value) of Methyl-Seq... |
| exampleMethyGenoSet | Example MethyGenoSet dataset |
| export.DMRInfo | Output the DMR (Differentially Methylated Region) data... |
| export.methyGenoSet | Export a MethyGenoSet object to be visualized using external... |
| filterBisulfiteVariant | filtering the variant calls of Bisulfite converted sequencing... |
| getContinuousRegion | Get continuous chromosome region by merging nearby or... |
| getCoverage | get the coverage based on a given GRanges object |
| 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) |
| MethyGenoSet-class | Class MethyGenoSet: contain and describe Illumina Infinium... |
| 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... |
| smoothMethyData | Smooth the methylation data |
| updateMethyGenoSet | Update old version MethyGenoSet objects |
