addMethPropCol          Add column for proportion of methylation
aggregateMethyl         Aggregate methylation data to get a summary
                        methylation profile for each region set
bigBinDT1               DNA methylation data for the "Applying MIRA to
                        a Biological Question" vignette (1st part).
bigBinDT2               DNA methylation data for the "Applying MIRA to
                        a Biological Question" vignette (2nd part).
binRegion               Divide region into similarly sized bins.
BSBinAggregate          Bins regions and aggregates methylation data
                        across the regions by bin
BSreadBiSeq             Read in files from biseq meth caller
bsseqToDataTable        Convert a BSseq object to data.table format for
                        MIRA.
calcMIRAScore           Score methylation profile based on its shape
exampleAnnoDT1          A data.table with annotation for a bisulfite
                        sample.
exampleAnnoDT2          Annotation data for the "Applying MIRA to a
                        Biological Question" vignette.
exampleBins             A data.table with artificial binned methylation
                        data
exampleBSDT             A data.table containing DNA methylation data.
exampleBSseqObj         A small BSseq object.
exampleRegionSet        A Granges object with Nrf1-binding regions.
MIRA                    Methylation-based Inference of Regulatory
                        Activity (MIRA)
plotMIRAProfiles        Plot summary methylation profile
plotMIRAScores          Plot MIRA scores and compare different
                        conditions
rbindNamedList          Combine data.tables from a named list into one
                        big data.table with extra column for name.
SummarizedExperimentToDataTable
                        Make MIRA-compatible data.tables using
                        information from SummarizedExperiment-based
                        classes
