All functions
addMethPropCol	Add column for proportion of methylation
aggregateMethyl	Aggregate methylation data to get a summary methylation profile for each region set
data	A data.table with binned methylation data for the first part of the "Applying MIRA to a Biological Question" vignette. Has data for 3 Ewing samples and 3 muscle-related samples (human skeletal myoblasts and other related samples). It is the product of `aggregateMethyl`.
data	A data.table with binned methylation data for the second part of the "Applying MIRA to a Biological Question" vignette. Has data for 12 Ewing samples and 12 muscle-related samples (human skeletal myoblasts and other related samples). It is the product of `aggregateMethyl`.
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.
data	A data.table with annotation for a bisulfite sample (name and sample type)
data	A data.table with annotation data for the "Applying MIRA to a Biological Question" vignette. Has annotation data (sampleName and sampleType columns) for 24 Ewing samples and 24 muscle-related samples (human skeletal myoblasts and other related samples).
data	A data.table with artificial binned methylation data
data	A data.table containing methylation data (position, number methylated reads and number of reads total) This object contains reduced representation bisulfite sequencing data from the GM06990 B-lymphoblastoid cell line that was generated by the ENCODE project (GEO accession GSE27584, sample GSM980583). Only a subset of the full data is used in this object and the data was switched from hg19 to hg38.
data	A BSseq object which has the top 20 rows of the BSseq object "BS.chr22" which was included as built-in data in the bsseq package
data	A GRanges object with a ranges corresponding to Nrf1 Chip-seq peaks in the GM12878 B-lymphoblastoid cell line (GEO accession GSE31477, sample GSM935309). Only a subset of the ranges are used in this object and the regions were switched from hg19 to hg38.
MIRA	Methylation-based Inference of Regulatory Activity (MIRA)
MIRAScore	Get MIRA score for each sample/region set combination
plotMIRAProfiles	Plot summary methylation profile
plotMIRAScores	Plot MIRA scores and compare different conditions
scoreDip	Score methylation profile based on its shape
SummarizedExperimentToDataTable	Make MIRA-compatible data.tables using information from SummarizedExperiment-based classes