geno.format

Convert a 4-column genotype matrix or data.frame into a simplified numerical format.

internal

Tools for the analysis of population differences
using the Major Histocompatibility Complex (MHC) genotypes of samples
having a variable number of alleles (1-4) recorded for each
individual.  A hierarchical Dirichlet-Multinomial model on the
genotype counts is used to pool small samples from multiple
populations for pairwise tests of equality.  Bayesian inference is
implemented via the 'rstan' package.  Bootstrapped and posterior
p-values are provided for chi-squared and likelihood ratio tests of
equal genotype probabilities.

Martin Lysy

MADPop

MHC Allele-Based Differencing Between Populations

Peter W.J. Kim

Terin Robinson

geno.format function

<dl><dt>X</dt>
<dd>Genotype matrix or data.frame.</dd>
<dt>Y.only</dt>
<dd>Logical. Whether or not to output only <code>Y</code> (see return).</dd></dl>

Arguments

Format genotype matrix — geno.format

<dl>

<dt>X</dt>
<dd>Genotype matrix or data.frame.</dd>


<dt>Y.only</dt>
<dd>Logical. Whether or not to output only <code>Y</code> (see return).</dd>

</dl>

geno.format: Format genotype matrix

Description

Usage

Value

Arguments