smoothMethyData {methyAnalysis} | R Documentation

## Smooth the methylation data

### Description

Smooth the methylation data by a sliding window with fixed width in bp unit

### Usage

    smoothMethyData(methyData, winSize = 250, lib = "FDb.InfiniumMethylation.hg19", p.value.detection.th = 0.05,
        bigMatrix=FALSE, dir.bigMatrix='.', savePrefix.bigMatrix=NULL, ...)

### Arguments

`methyData` | A GenoSet or MethyLumiM object
`winSize` | Half sliding window size in bp unit at each side of the probe
`lib` | Methylation annotation library
`p.value.detection.th` | the threshold of detection p.value used to determine the failed probes, which will be set as NAs.
`bigMatrix` | whether to save the data as BigMatrix (designed for very large dataset)
`dir.bigMatrix` | the parent directory to save the BigMatrix data files
`savePrefix.bigMatrix` | the folder name prefix of the directory to save the BigMatrix data files. The fold name will be like this: paste(savePrefix.bigMatrix, '_bigmat', sep=”)
`...` | other parameters

### Details

The function basically averages the probes within a local window (within winSize bp at each side of the probe).

### Value

An object with the methylation values smoothed

### Author(s)

Pan Du

### See Also

`detectDMR.slideWin`

### Examples

    data(exampleMethyGenoSet)
    smoothData <- smoothMethyData(exampleMethyGenoSet)

[Package methyAnalysis version 1.26.0 Index]