estimateBeta: Estimate methylation Beta-value matrix

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Description

Estimate methylation Beta-value matrix from MethyLumiM-class object or eSet-class object, which include methylated and unmethylated probe intensities

Usage

estimateBeta(methyLumiM, returnType=c("ExpressionSet", "matrix"), offset = 100)

Arguments

methyLumiM	MethyLumiM-class object or eSet-class object, which include methylated and unmethylated probe intensities
returnType	determine whether return an ExpressionSet or matrix object
offset	An offset value added to the denominator to avoid close to zero intensities

Details

Beta-value is ratio between Illumina methylated probe intensity and total probe intensities (sum of methylated and unmethylated probe intensities, see estimateIntensity). An offset value added to the denominator to avoid close to zero intensities in the denominator. Beta-value is in the range of 0 and 1. If we assume the probe intensity follows Gamma distribution, then the Beta-value follows a Beta distribution.

Value

An ExpressionSet or matrix object of methylation Beta-value

Author(s)

Pan DU

See Also

See Also as estimateIntensity and estimateM

Examples

data(example.lumiMethy)
methyLumiBeta = estimateBeta(example.lumiMethy)
density(methyLumiBeta)

lumi documentation built on Nov. 8, 2020, 5:27 p.m.