Methylation-Based Inference of Regulatory Activity

Documentation for package ‘MIRA’ version 1.31.0

MIRA-package	Methylation-based Inference of Regulatory Activity (MIRA)
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