detectDMR.slideWin {methyAnalysis} | R Documentation |
Detect DMR (Differentially Methylated Region) using slide window smoothing
detectDMR.slideWin(methyGenoSet, sampleType, winSize = 250, testMethod = c("ttest", "wilcox"), p.adjust.method = "fdr", p.value.detection.th = 0.05, ...)
methyGenoSet |
A GenoSet object includes the methylation data information |
sampleType |
A vector shows the sample type information |
winSize |
Slide window size (half window size, bp at each side of the probe) |
testMethod |
test methods |
p.adjust.method |
p.value FDR adjust method |
p.value.detection.th |
the threshold of detection p.value used to determine the failed probes, which will be set as NAs. |
... |
other paramters |
The function will check whether the data was previously smoothed. If not, slide-window smoothing will be performed first, and then followed by differential methylation tests
A GRanges object with additional test information (difference, p.value, p.adjust, and etc.)
Pan Du
data(exampleMethyGenoSet) sampleType <- colData(exampleMethyGenoSet)$SampleType ## Do differential test allResult <- detectDMR.slideWin(exampleMethyGenoSet, sampleType=sampleType, testMethod='ttest') head(allResult)