Characterization of Methylation using positional ENTanglement

Documentation for package ‘CMEnt’ version 0.99.15

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annotateDMRsWithGenes	Annotate DMRs with Gene Information
augmentBSSeq	Augment BSseq Object
buildDMRs	Build Differentially Methylated Regions (DMRs) from Differentially Methylated Positions (seeds)
combinePvalues	Combine spatially correlated p-values with comb-p style SLK correction
computeDMRsInteraction	Compute Motif-Based DMR Interactions
convertBetaToTabix	Convert Beta File to Tabix-Indexed Format
extractDMRMotifs	Extract DMR Motif Frequencies
findDMPsArray	Find DMPs from methylation array beta values using limma
findDMPsBSSeq	Find DMPs using DSS on BSseq objects
getBetaHandler	Create a BetaHandler object for efficient beta value access
getDMRSequences	Extract DNA Sequences for DMRs
getSortedGenomicLocs	Get Sorted Array Locations
launchCMEntViewer	Launch CMEnt Interactive Viewer
loadExampleInputData	Load CMEnt Example Resources
loadExampleInputDataChr21And22	Load CMEnt Example Resources
loadExampleInputDataChr5And11	Load CMEnt Example Resources
orderByLoc	Orders a vector of indices according to their corresponding genomic locations (chromosome and position). This function is useful for sorting site sites or other genomic features by their physical positions.
plotAutoDMRsCircos	Plot DMR Circos Views Using Automatically Selected Regions
plotDMR	Plot DMR
plotDMRBlockFormation	Plot Intermediate DMR Block Formation Diagnostics
plotDMRs	Plot Multiple DMRs in a Grid
plotDMRsCircos	Plot Circos Visualization of DMRs
plotDMRsManhattan	Plot Manhattan-Style View of DMR Scores
readCustomMethylationBedData	Read and Process Custom Methylation BED Data
reduceBSseqAroundSeeds	Reduce BSseq object around seed locations
scoreDMRs	Add Complementary Classification Scores to DMRs
simulateDMRs	Simulate DMRs while preserving local methylation structure
sortBetaFileByCoordinates	Sort Beta File by Genomic Coordinates
sparsifySeeds	Sparsify seed locations by minimum distance