methyAnalysis (version 1.14.0)

smoothMethyData: 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

Value

An object with the methylation values smoothed

Details

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

See Also

detectDMR.slideWin

Examples

data(exampleMethyGenoSet)
smoothData <- smoothMethyData(exampleMethyGenoSet)