Differentially Methylated Regions Caller

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Documentation for package ‘DMRcaller’ version 1.41.2

• 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
analyseReadsInsideRegionsForConditionPMD	Analyse reads inside regions for condition
computeCoMethylation	Compute pairwise co-methylation statistics for cytosine sites within regions
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
computePMDs	Compute PMDs
computeVMDs	Compute VMDs
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
filterPMDs	Filter PMDs
filterVMDs	Filter VMDs
filterVMRsONT	Filter VMRs for ONT Data
GEs	The genetic elements data
GEs_hg38	The genetic elements data of GRCh38 Genome Reference
getWholeChromosomes	Get whole chromosomes from methylation data
joinReplicates	Joins together two GRange objects in a single containing all the replicates
mergeDMRsIteratively	Merge DMRs iteratively
mergePMDsIteratively	Merge PMDs iteratively
methylationDataList	The methylation data list
ontSampleGRangesList	The ONT methylation data list
ont_gr_GM18870_chr1_PMD_bins_1k	Partially Methilated Domains example
ont_gr_GM18870_chr1_sorted_bins_1k	The ONT methylation data example
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
PMDsBinsCG	The PMDs between GM18501 and GM18876 using Bins method
PMDsNoiseFilterCG	The PMDs between GM18501 and GM18876 using Noise_filter method
poolMethylationDatasets	Pool methylation data
poolTwoMethylationDatasets	Pool two methylation datasets
readBismark	Read Bismark
readBismarkPool	Read Bismark pool
readONTbam	Load ONT BAM, decode MM/ML, and count modified vs. unmodified reads
saveBismark	Save Bismark
scanBamChr1Random5	The bam file from ONT nanopore .pod5 files
selectCytosine	Select Cytosine Positions
syntheticDataReplicates	Simulated data for biological replicates