getB: Extract methylation Beta values.

In xuz1/ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Extract methylation Beta values.

Description

Extract Methylation Beta value, Beta = Meth / (Meth + Unmeth + offset)

Usage

getB(mdat,type="Illumina",offset=100)

Arguments

mdat	An object of class methDataSet or MethylSet.
type	type="Illumina" sets offset=100 as per Genome Studio software.
offset	Regularization factor in calculating beta ratio, 100 in default

Value

Methylation Beta value = Meth / (Meth + Unmeth + offset). Meth is methylated intensity matrix, Unmeth is unmethylated intensity matrix.

Author(s)

Zongli Xu

Examples

if (require(minfiData)){
path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,recursive = TRUE)
mdat=getmeth(rgSet)
beta=getB(mdat,"Illumina")
}

xuz1/ENmix documentation built on Nov. 24, 2024, 4:31 a.m.