Package index • CMEnt

Differential Methylation Analysis

buildDMRs(): Build Differentially Methylated Regions (DMRs) from Differentially Methylated Positions (seeds)
scoreDMRs(): Add Complementary Classification Scores to DMRs
findDMPsArray(): Find DMPs from methylation array beta values using limma
findDMPsBSSeq(): Find DMPs using DSS on BSseq objects
simulateDMRs(): Simulate DMRs while preserving local methylation structure

BetaHandler: Beta Handler Class
getBetaHandler(): Create a BetaHandler object for efficient beta value access
convertBetaToTabix(): Convert Beta File to Tabix-Indexed Format
sortBetaFileByCoordinates(): Sort Beta File by Genomic Coordinates
readCustomMethylationBedData(): Read and Process Custom Methylation BED Data
augmentBSSeq(): Augment BSseq Object
loadExampleInputData() loadExampleInputDataChr5And11() loadExampleInputDataChr21And22(): Load CMEnt Example Resources
getSortedGenomicLocs(): Get Sorted Array Locations
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.

annotateDMRsWithGenes(): Annotate DMRs with Gene Information
combinePvalues(): Combine spatially correlated p-values with comb-p style SLK correction
getDMRSequences(): Extract DNA Sequences for DMRs
extractDMRMotifs(): Extract DMR Motif Frequencies
computeDMRsInteraction(): Compute Motif-Based DMR Interactions

plotDMR(): Plot DMR
plotDMRs(): Plot Multiple DMRs in a Grid
plotDMRBlockFormation(): Plot Intermediate DMR Block Formation Diagnostics
plotDMRsManhattan(): Plot Manhattan-Style View of DMR Scores
plotDMRsCircos(): Plot Circos Visualization of DMRs
plotAutoDMRsCircos(): Plot DMR Circos Views Using Automatically Selected Regions
launchCMEntViewer(): Launch CMEnt Interactive Viewer

CMEnt CMEnt-package: CMEnt: Characterization of Methylation using positional ENTanglement