B2M: Converting methylation beta value to M value.

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

Converting methylation beta value to M value.

Description

Convert methylation beta value to M value.

Usage

B2M(x)

Arguments

x	An numeric matrix with values between 0 and 1

Details

Methylation beta value is calculated as beta=M/(M+U+a). M is methylated intensity, U is unmethylated intensity, and a is a constant offset (by default , a=100). M value is calculated as M=log2((M+a)/(U+a)). M or U is usually greater than 1000, so a is negligible for most probes. if a=0, then M=log2(beta)/(1-beta).

Value

A matrix of M values

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")
m=B2M(beta)
}

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