detectDMR.slideWin: Detect DMR (Differentially Methylated Region) using slide...

In methyAnalysis: DNA methylation data analysis and visualization

Description

Detect DMR (Differentially Methylated Region) using slide window smoothing

Usage

detectDMR.slideWin(methyGenoSet, sampleType, winSize = 250, testMethod = c("ttest", "wilcox"), 
  p.adjust.method = "fdr", p.value.detection.th = 0.05, ...)

Arguments

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

Details

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

Value

A GRanges object with additional test information (difference, p.value, p.adjust, and etc.)

Author(s)

Pan Du

See Also

identifySigDMR

Examples

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

methyAnalysis documentation built on Nov. 8, 2020, 8:09 p.m.