getContinuousRegion {methyAnalysis} | R Documentation |
Get continuous chromosome region by merging nearby or overlapping regions
getContinuousRegion(detectResult, scoreColumns = NULL, scoreFuns = c(mean=mean), maxGap = 2000, minGap = 100)
detectResult |
A GRanges object (with "status" column) or a data.frame with "CHROMOSOME", "POSITION" and "status" columns |
scoreColumns |
The numeric score columns to be summarized in DMR |
scoreFuns |
A named vector of summarizing functions. The vector names will be used in the output columns |
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 |
The "status" column in the "detectRsult" parameter is required, which is a logical vector indicating the interested probes.
A GRanges object of DMR
Pan Du
data(exampleMethyGenoSet) ## get sample type information sampleType <- colData(exampleMethyGenoSet)$SampleType ## Do differential test allResult <- detectDMR.slideWin(exampleMethyGenoSet, sampleType=sampleType, testMethod='ttest') ## Identify the DMR (Differentially Methylated Region) by setting proper parameters. ## Here we simply using fdr.adjusted p.value cutoff 0.05 to define DMR ## "status" column is required for getContinuousRegion function. values(allResult)$status <- values(allResult)$p.adjust < 0.05 dmrInfo <- getContinuousRegion(allResult)