estimateBeta {lumi} | R Documentation

## Estimate methylation Beta-value matrix

### 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)

[Package lumi version 2.36.0 Index]