# Methylation-Based Inference of Regulatory Activity

## Documentation for package ‘MIRA’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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