consolidateDMRs {methylPipe} | R Documentation

## 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

### 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.

### Value

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

### Author(s)

Kamal Kishore

### See Also

`findDMR`

### Examples

    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

[Package methylPipe version 1.16.0 Index]