consolidateDMRs: Consolidating Differentially Methylated Regions (DMRs)

Description

Joins differentially methylated regions according to their proximity to each other, statistical significance and methylation difference

Usage

consolidateDMRs(DmrGR, pvThr=0.05, MethDiff_Thr=NULL, log2Er_Thr =NULL, GAP=0, type=NULL, correct=FALSE)

Arguments

DmrGR

the GRanges object resulting from the findDMR function

pvThr

numeric; the minimum pvalue for a DMR to be selected

MethDiff_Thr

numeric; the absolute value of minimum methylation difference percentage (for both hyper- and hypo-methyaltion) cutoff for the selection of a DMR

log2Er_Thr

numeric; the absolute value of minimum log2Enrichment (for both hyper- and hypo-methyaltion) cutoff for the selection of a DMR

GAP

numeric; the minimum distance between two adjacent DMRs; DMRs closer than that will be joined, resulting DMRs will be updated mean methylation difference and Pvalues combined using the Fisher's Method

type

character; one of the "hyper" or "hypo", specifies the type of differentially menthylated regions selected

correct

logical; whether to correct the pvalues using the Benjamini-Hochberg muliple testing correction method

Value

Either NULL or a GRanges object containing the differential methylated regions satisfying the criteria.

Details

After the DMRs are identified by findDMR method, a consolidation can be applied on them. This functions allows to select hyper/hypo differentially methylated regions based on P-value and absolute methylation change thresholds. Moreover, DMRs closer than a given distance can be joined. The final GRanges object with the set of final DMRs will be provided with updated mean methylation difference and Pvalues combined using the Fisher's Method.

Examples

Run this code

DMRs_file <- system.file('extdata', 'DMRs.Rdata', package='methylPipe')
load(DMRs_file)
hyper.DMRs.conso <- consolidateDMRs(DmrGR=DMRs, pvThr=0.05, GAP=100, type="hyper", correct=TRUE)
hyper.DMRs.conso