pa_sim: Simulate transmission Presence absence 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 presence absence 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 simulatin the whole data set each pair should be run separately as to not use the same bottleneck

Usage

pa_sim(data, lambda)

Arguments

data	a data frame with with chr,pos,freq1, and pair_id columns
lambda	The lambda of the zero truncated Poisson

Value

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

Examples

pa_sim(small_trans,1.3)

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