meanDiff {dmrseq} | R Documentation

## Function to compute raw mean methylation differences

### Description

This function calculates raw mean methylation differences for the covariate of interest over a set of DMRs (or regions of interest), assuming a simple two-group comparison.

### Usage

    meanDiff(bs, dmrs, testCovariate)

### Arguments

`bs` | a `BSseq` object
`dmrs` | a data.frame with one row per DMR. This can be in the format of `dmrseq` output, but at least should contain the indexStart and indexEnd values of the regions of interest.
`testCovariate` | a character indicating the covariate of interest in the `pData` slot of `bs`.

### Value

numeric vector of raw mean methylation differences.

### Examples

    data(BS.chr21)
    data(dmrs.ex)
    rawDiff <- meanDiff(BS.chr21, dmrs=dmrs.ex, testCovariate="CellType")

[Package dmrseq version 1.7.3 Index]