L.Nb.beta: Betabinomial Likelihood functions

In jtmccr1/HIVEr: Analysis of transmission and intrahost iSNV data taken as part of the HIVE cohort

Description

What is the probability of observing the data given a bottleneck size under the beta binomial model. This is a wrapper around the two likelihood functions

Usage

like_found.beta(v_r, v_d, Nb, gc_ul, threshold, acc = accuracy_stringent)

like_lost.beta.uncert(v_r, v_d, Nb, gc_ul, threshold,
  acc = accuracy_stringent)

L.Nb.beta(v_r, v_d, Nb, gc_ul, threshold, acc = accuracy_stringent)

Arguments

v_r	allele frequency in the recipient
v_d	allele frequency in the donor
Nb	Bottleneck size (may be a vector)
gc_ul	titer in recipeint sample
threshold	detection level threshold
acc	a data frame with accrucacy data must contain, columns freq,sensitivity, and gc_ul

Value

The likelihood of observing the data given the bottleneck size.

Functions

• like_found.beta: likelihood the variant is found in recipient

• like_lost.beta.uncert: likelihood the variant is not found in recipient

jtmccr1/HIVEr documentation built on May 29, 2019, 1:50 a.m.