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) MIRA is a score that infers regulatory activity of genomic elements based on DNA methylation data. It assess the degree of dip in methylation level surrounding a regulatory site of interest, such as transcription factor binding sites. This package provides functions for aggregating methylation data across region sets, in bins.

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