bsseqToDataTable: Convert a BSseq object to data.table format for MIRA.

In databio/MIRA: Methylation-Based Inference of Regulatory Activity

Description

Converts a BSseq object to a list of data.tables with one data.table per sample. A wrapper of the SummarizedExperimentToDataTable function.

Usage

bsseqToDataTable(BSseqObj)

Arguments

BSseqObj

An object of class BSseq, can have smoothed or raw methylation data.

Value

MIRAFormatBSDTList A list of data.tables containing the methylation data. One data.table per sample with the column names: 'chr', 'start' (methylation coordinate), 'methylCount' (number of methylated reads), 'coverage' (total number of reads), and 'methylProp' (proportion of methylated reads). The order of the list is the order of samples in the columns of the BSseq object. If sample names are in the BSseq object, then a named list will be returned.

Examples

data("exampleBSseqObj")
MIRAFormatBSDTList <- bsseqToDataTable(exampleBSseqObj)

databio/MIRA documentation built on April 16, 2020, 9:53 p.m.