detectDMR.slideWin {methyAnalysis} | R Documentation

## Detect DMR (Differentially Methylated Region) using slide window smoothing

### 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)

[Package methyAnalysis version 1.30.0 Index]