betabin_sim: Simulate transmission Beta binomial model

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

Description

Simulate the transmission of alleles using the betabinomial model. Essentially this takes the frequency of the variant allele, and bottleneck size and simulates the found column. It also selects a bottleneck size based on lambda and a zero truncated Poisson. If simulation the whole data set each pair should be run separately as to not use the same bottleneck

Usage

betabin_sim(data, lambda, threshold, acc = accuracy_stringent)

Arguments

data	a data frame with with chr,pos,freq1, and pair_id columns
lambda	The lambda of the zero truncated Poisson
threshold	limit of variant calling detection
acc	a data frame with accuracy metrics

Value

data frame the same as data but with a simulated found column

Examples

betabin_sim(small_trans,1.2,0.02,accuracy_stringent)

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