rundEploid: Wrapper function for dEploid

In Ahhgust/MMDIT: Mitochondrial mixture project

Description

This function takes information on alternate and reference allele counts, number of individuals and the recombination rate and runs the dEploid function on them. It retuns the dEploid output with includes estimated haplotypes, mixture proprotions and other phasing statistics. Additionaly this function also returns a list of nucleotide positions that violate the infinte sites model.

Usage

rundEploid(AR, long, NumMCMC = 800, exportPostProb = TRUE, recomb = 0, k = 5)

Arguments

AR	Table of alternate and reference allele counts (Empop2AltRef object)
long	Table with information on sample ID, position, allele and type of mutation
NumMCMC	A numeric argument that tells the function the number of MCMC samples (default value 800)
exportPostProb	Save the posterior probabilities of the final iteration of all individuals
recomb	numeric argument that gives the function the constant recombination probability (default value of 0.0)
k	A numeric argument that tells the function the number of individuals in the mixture (default value 5, maximum of 5)

Examples

## Not run: 
rundEploid(AR, long, NumMCMC=3000, exportPostProb, recomb=0.0, k=5)

## End(Not run)

Ahhgust/MMDIT documentation built on Jan. 27, 2021, 11:48 a.m.