genind_to_structure

<p>The function converts an object of class <code>genind</code> into
a STRUCTURE file.
It is designed to be used with diploid microsatellite data with
alleles coded with 2 or 3 digits or SNPs genind objects.</p>

internal

Build graphs for landscape genetics analysis. This set of
functions can be used to import and convert spatial and genetic data
initially in different formats, import landscape graphs created with
'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>,
make diagnosis plots of isolation by distance relationships in order to
choose how to build genetic graphs, create graphs with a large range of
pruning methods, weight their links with several genetic distances, plot
and analyse graphs,	compare them with other graphs. It uses functions from
other packages such as 'adegenet'
(Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi
et Nepusz, 2006) <https://igraph.org/>. It also implements methods
commonly used in landscape genetics to create graphs, described by Dyer et
Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et
Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data
(van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.

Paul Savary

graph4lg

Build Graphs for Landscape Genetics Analysis

Gilles Vuidel

Tyler Rudolph

Alexandrine Daniel

genind_to_structure function

<dl><p></p><p><dt>x</dt>
<dd><p>An object of class <code>genind</code>
from package <span class="pkg">adegenet</span>.</p></dd></p><p>
<dt>output</dt>
<dd><p>A character string of the form 
<code>output = "path_to_file/file_name.txt"</code>. Then, the function
will write a text file named 'file_name.txt' in the directory corresponding
to 'path_to_file'. Without 'path_to_file', the text file is written in the
current working directory. The text file has the format required by STRUCTURE
software.</p></dd></p><p></p></dl>

Arguments

<p></p><p><div class="section" id="allele-coding">
<h3>Allele coding</h3>
<p>This function can handle genetic data with different allele coding: 2 or 3
digit coding for microsatellite data or 2 digit coding for SNPs (A,C,T,G
become respectively 01, 02, 03, 04).</p>
</div>
<div class="section" id="individuals-order">
<h3>Individuals order</h3>
<p>When individuals in input data are not ordered by populations, individuals
from the same population can be separated by individuals from other
populations. It can be problematic when calculating then pairwise distance
matrices. Therefore, in such a case, individuals are ordered by populations
and populations ordered in alphabetic order.</p>
</div>
</p>

Warning

Author

Convert a genind object into a STRUCTURE file — genind_to_structure

<dl>

<dt>x</dt>
<dd><p>An object of class <code>genind</code>
from package <span class="pkg">adegenet</span>.</p></dd>


<dt>output</dt>
<dd><p>A character string of the form 
<code>output = "path_to_file/file_name.txt"</code>. Then, the function
will write a text file named 'file_name.txt' in the directory corresponding
to 'path_to_file'. Without 'path_to_file', the text file is written in the
current working directory. The text file has the format required by STRUCTURE
software.</p></dd>

</dl>



<div class='section' id='allele-coding'>
<h3>Allele coding</h3>
<p>This function can handle genetic data with different allele coding: 2 or 3
digit coding for microsatellite data or 2 digit coding for SNPs (A,C,T,G
become respectively 01, 02, 03, 04).</p>
</div>
<div class='section' id='individuals-order'>
<h3>Individuals order</h3>
<p>When individuals in input data are not ordered by populations, individuals
from the same population can be separated by individuals from other
populations. It can be problematic when calculating then pairwise distance
matrices. Therefore, in such a case, individuals are ordered by populations
and populations ordered in alphabetic order.</p>
</div>


genind_to_structure: Convert a genind object into a STRUCTURE file

Description

Usage

Value

Arguments

Warning

Allele coding

Individuals order

Author

Examples