identifySigDMR: Identify significantly DMR (Differentially Methylated Region)
In methyAnalysis: DNA methylation data analysis and visualization

Description Usage Arguments Details Value Author(s) See Also Examples

Identify significantly DMR (Differentially Methylated Region)

1	identifySigDMR(detectResult, p.adjust.method = "fdr", pValueTh = 0.01, fdrTh = pValueTh, diffTh = 1, minProbeNum = 1, maxGap = 2000, minGap=100, oppositeMethylation = FALSE, topNum = NULL)

`detectResult`	A GRanges object or a data.frame with "PROBEID", "CHROMOSOME" and "POSITION" columns
`p.adjust.method`	p.value FDR adjust method
`pValueTh`	The threshold of p.value
`fdrTh`	The threshold of FDR (adjusted p.value)
`diffTh`	The threshold of difference between two conditions
`minProbeNum`	Minimum number of probes in each DMR
`maxGap`	The maximum gap allowed between two nearby probes to be considered within a same DMR
`minGap`	If two nearby DMRs have a gap less than or equal to the minGap, they will be merged as a single DMR
`oppositeMethylation`	Whether require the averaged methylation levels in the DMR are in opposite direction
`topNum`	Whether only returns the top number of probes (ranked by p.value)

(with "status" column)

We define a differentially methylated region (DMR) as a region, in which most measured CpG-sites are differentially methylated. To identify DMRs, the function first determines the differential methylation status of each probe, then merge them as a continuous region. The identifySigDMR function returns a list of two GRanges objects. The sigDMRInfo includes the identified DMRs, and the sigDataInfo includes all differentially methylated probe information.

A list of GRanges objects, sigDMRInfo and sigDataInfo. sigDMRInfo contains DMR information, while sigDataInfo includes the probe level information within the DMRs.

Pan Du

getContinuousRegion, annotateDMRInfo

	data(exampleMethyGenoSet)
	
	sampleType <- colData(exampleMethyGenoSet)$SampleType
	
	## Do differential test
	allResult <- detectDMR.slideWin(exampleMethyGenoSet, sampleType=sampleType, testMethod='ttest')

	## Identify the DMR (Differentially Methylated Region) by setting proper parameters.
	## Here we just use default ones
	allDMRInfo <- identifySigDMR(allResult)