estimateBeta: Estimate methylation Beta-value matrix

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/methylation_preprocessing.R

Description

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

Usage

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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

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

lumi documentation built on May 31, 2017, 11:53 a.m.

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