identifySigDMR {methyAnalysis} | R Documentation

## Identify significantly DMR (Differentially Methylated Region)

### Description

Identify significantly DMR (Differentially Methylated Region)

### Usage

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

### Arguments

`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)

### Details

(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.

### Value

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

### Author(s)

Pan Du

### See Also

`getContinuousRegion`, `annotateDMRInfo`

### Examples

    	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)

[Package methyAnalysis version 1.30.0 Index]