calcAfreq: Calculate Allele Frequencies

In innager/dcifer: Genetic Relatedness Between Polyclonal Infections

Calculate Allele Frequencies

Description

Calculates population allele frequencies from data, adjusting for COI.

Usage

calcAfreq(dsmp, coi, tol = 1e-04, qstart = 0.5)

Arguments

dsmp	a list with each element corresponding to one sample.
coi	a vector containing complexity of infection for each sample.
tol	convergence tolerance for frequency estimates.
qstart	a starting value for frequencies.

Value

A list of allele frequencies, where each element is a numeric vector containing frequencies for a single locus.

Examples

coi   <- getCOI(dsmp, lrank = 2)           # estimate COI first
afreq <- calcAfreq(dsmp, coi, tol = 1e-5)

innager/dcifer documentation built on May 21, 2024, 1:23 a.m.