# Differentially Methylated Regions caller

## Documentation for package ‘DMRcaller’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

DMRcaller-package | Call Differentially Methylated Regions (DMRs) between two samples
analyseReadsInsideRegionsForCondition | Analyse reads inside regions for condition
computeDMRs | Compute DMRs
computeDMRsReplicates | Compute DMRs
computeMethylationDataCoverage | Compute methylation data coverage
computeMethylationDataSpatialCorrelation | Compute methylation data spatial correlation
computeMethylationProfile | Compute methylation profile
computeOverlapProfile | Compute Overlaps Profile
DMRcaller | Call Differentially Methylated Regions (DMRs) between two samples
DMRsNoiseFilterCG | The DMRs between WT and met1-3 in CG context
extractGC | Extract GC
filterDMRs | Filter DMRs
GEs | The genetic elements data
getWholeChromosomes | Get whole chromosomes from methylation data
joinReplicates | Joins together two GRange objects in a single containing all the replicates
mergeDMRsIteratively | Merge DMRs iteratively
methylationDataList | The methylation data list
plotLocalMethylationProfile | Plot local methylation profile
plotMethylationDataCoverage | Plot methylation data coverage
plotMethylationDataSpatialCorrelation | Plot methylation data spatial correlation
plotMethylationProfile | Plot Methylation Profile
plotMethylationProfileFromData | Plot methylation profile from data
plotOverlapProfile | Plot overlap profile
poolMethylationDatasets | Pool methylation data
poolTwoMethylationDatasets | Pool two methylation datasets
readBismark | Read Bismark
readBismarkPool | Read Bismark pool
saveBismark | Save Bismark
syntheticDataReplicates | Simulated data for biological replicates