r4_functions

This group of functions is called by <code>linkage</code>.

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

r4_functions function

<dl><dt>x</dt>
<dd>A frequency table of the different classes of dosages in the progeny. The column names start with <code>"n_"</code>. Followed by the dosage of the first marker and then of the second.</dd>
<dt>ncores</dt>
<dd>Number of cores to use for parallel processing (deprecated).</dd></dl>

Arguments

Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid — r4_functions

<dl>

<dt>x</dt>
<dd>A frequency table of the different classes of dosages in the progeny. The column names start with <code>"n_"</code>. Followed by the dosage of the first marker and then of the second.</dd>


<dt>ncores</dt>
<dd>Number of cores to use for parallel processing (deprecated).</dd>

</dl>

r4_functions: Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid

Description

Value

Arguments