negll

size

Theoretical probability for heterozygous is 0.5, for homozygous is 0.999

prob

Rho parameter of Beta-Binomial distribution of alternative allele

Calculates negative log likelihood for beta binomial distribution.

Imports Variant Calling Format file into R. It can detect
whether a sample contains contaminant from the same species.
In the first stage of the approach, a change-point detection
method is used to identify copy number variations for filtering.
Next, features are extracted from the data for a support vector
machine model. For log-likelihood calculation, the deviation
parameter is estimated by maximum likelihood method. Using
a radial basis function kernel support vector machine, the
contamination of a sample can be detected.

negll: Negative Log Likelihood

Description

Usage

Arguments