PCA_progeny

Principal component analysis in order to identify individuals that deviate from the population.

Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0,
both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) <doi:10.1007/s00122-021-03834-x>.

Peter Bourke

polymapR

Linkage Analysis in Outcrossing Polyploids

Geert van Geest

Roeland Voorrips

Yanlin Liao

PCA_progeny function

<dl><dt>dosage_matrix</dt>
<dd>An integer matrix with markers in rows and individuals in columns.</dd>
<dt>highlight</dt>
<dd>A list of character vectors specifying individual names that should be highlighted</dd>
<dt>colors</dt>
<dd>Highlight colors. Vector of the same length as <code>highlight</code>.</dd>
<dt>log</dt>
<dd>Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.</dd></dl>

Arguments

Perform a PCA on progeny — PCA_progeny

<dl>

<dt>dosage_matrix</dt>
<dd>An integer matrix with markers in rows and individuals in columns.</dd>


<dt>highlight</dt>
<dd>A list of character vectors specifying individual names that should be highlighted</dd>


<dt>colors</dt>
<dd>Highlight colors. Vector of the same length as <code>highlight</code>.</dd>


<dt>log</dt>
<dd>Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.</dd>

</dl>

PCA_progeny: Perform a PCA on progeny

Description

Usage

Arguments

Details

Examples