estimateBeta {lumi} | R Documentation |
Estimate methylation Beta-value matrix from MethyLumiM-class object or eSet-class object, which include methylated and unmethylated probe intensities
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
data(example.lumiMethy) methyLumiBeta = estimateBeta(example.lumiMethy) density(methyLumiBeta)