getAvgLL

Hom MLE of p in Beta-Binomial model, default is 0.9981416 from NA12878_1_L5

hom_mle

Het MLE of p in Beta-Binomial model, default is 0.4737897 from NA12878_1_L5

het_mle

Hom MLE of rho in Beta-Binomial model, default is 0.04570275 from NA12878_1_L5

hom_rho

Het MLE of rho in Beta-Binomial model, default is 0.02224098 from NA12878_1_L5

het_rho

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.

getAvgLL: Calculate average log-likelihood

Description

Usage

Arguments

Value