smoothMethyData: Smooth the methylation data

In methyAnalysis: DNA methylation data analysis and visualization

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)

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