identifySigDMR {methyAnalysis} | R Documentation |
Identify significantly DMR (Differentially Methylated Region)
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)