gen2dist

Converts variant-call (VCF) genotype data into a matrix of pairwise genetic
distances between samples.

Provides a framework for the measurement and partitioning of
the (similarity-sensitive) biodiversity of a metacommunity and its
constituent subcommunities. Richard Reeve, et al. (2016)
<doi:10.48550/arXiv.1404.6520>.

Richard Reeve

rdiversity

Measurement and Partitioning of Similarity-Sensitive
Biodiversity

Sonia Mitchell

Tom White

gen2dist function

<dl><dt>vcf</dt>
<dd>object of class <code>data.frame</code> laid out like the body of a VCF
file: a column named <code>FORMAT</code> followed by one column per sample, whose
entries begin with the genotype (e.g. <code>"0|0"</code>, <code>"0|1"</code>,
<code>"1|1"</code>). Such a <code>data.frame</code> can be obtained, for example, from
the <code>gt</code> element of a <code>vcfR</code> object read in with
<code>vcfR::read.vcfR()</code>.</dd>
<dt>biallelic</dt>
<dd>logical describing whether the data is biallelic or not (default).</dd></dl>

Arguments

Genetic distance matrix — gen2dist

<dl>

<dt>vcf</dt>
<dd>object of class <code>data.frame</code> laid out like the body of a VCF
file: a column named <code>FORMAT</code> followed by one column per sample, whose
entries begin with the genotype (e.g. <code>"0|0"</code>, <code>"0|1"</code>,
<code>"1|1"</code>). Such a <code>data.frame</code> can be obtained, for example, from
the <code>gt</code> element of a <code>vcfR</code> object read in with
<code>vcfR::read.vcfR()</code>.</dd>


<dt>biallelic</dt>
<dd>logical describing whether the data is biallelic or not (default).</dd>

</dl>

gen2dist: Genetic distance matrix

Description

Usage

Value

Arguments