Consolidating Differentially Methylated Regions (DMRs)
Description
Joins differentially methylated regions according to their proximity to each other, statistical significance and methylation difference
Usage
1 
Arguments
DmrGR 
the GRanges object resulting from the

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 hypomethyaltion) cutoff for the selection of a DMR 
log2Er_Thr 
numeric; the absolute value of minimum log2Enrichment (for both hyper and hypomethyaltion) 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 BenjaminiHochberg 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 Pvalue 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
1 2 3 4  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
