meanDiff: Function to compute raw mean methylation differences

In dmrseq: Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

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")

dmrseq documentation built on April 18, 2021, 6 p.m.