mbmix_loglik {mbmixture}

log likelihood function for microbiome mixture

Description

Calculate log likelihood function for microbiome sample mixture model at particular values of p and e.

Usage

mbmix_loglik(tab, p, e = 0)

Arguments

tab

Dataset of read counts as 3d array of size 3x3x2, genotype in first sample x genotype in second sample x allele in read.

p

Contaminant probability (proportion of mixture coming from the second sample).

e

Sequencing error rate.

Value

The log likelihood evaluated at p and e.

Examples

data(mbmixdata)
mbmix_loglik(mbmixdata, p=0.74, e=0.002)