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

View source: R/methylation_preprocessing.R

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

1 | ```
estimateBeta(methyLumiM, returnType=c("ExpressionSet", "matrix"), offset = 100)
``` |

`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 |

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.

An ExpressionSet or matrix object of methylation Beta-value

Pan DU

See Also as `estimateIntensity`

and `estimateM`

1 2 3 | ```
data(example.lumiMethy)
methyLumiBeta = estimateBeta(example.lumiMethy)
density(methyLumiBeta)
``` |

lumi documentation built on Nov. 17, 2017, 8:58 a.m.

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