math_fit: The probability of lambda for a loci

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

Description

The probability of observing the data given lambda and the presence absence model.In this fit we take the minority frequency to be correct

Usage

math_fit(data, Nb_max, model, threshold, acc)

Arguments

data	a data frame of one donor polymorphic loci. It must have columns chr,pos,freq1, and found
Nb_max	The maximum bottleneck size to test
model	The model we are using must be either "PA" or "BetaBin"
threshold	limit of variant calling detection
acc	a data frame with accuracy metrics

Value

a tibble with columns for each lambda and the probability of observing the data for that site.

Examples

get_freqs(c("HS1595","HS1563"),small_isnv)->small_dups
polish_freq(small_dups,freq1,0.02)->x
x$found=c(TRUE,TRUE)
math_fit(x,100,"PA")
x$found=c(FALSE,TRUE)
math_fit(x,100,"PA")

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