Differentially Methylated Regions caller


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Documentation for package ‘DMRcaller’ version 1.12.7

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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