design_connectivity

Determine the connected parts of a MPP design using the method of Weeks and
Williams (1964) and the package igraph.

Analysis of experimental multi-parent populations to detect regions
of the genome (called quantitative trait loci, QTLs) influencing
phenotypic traits measured in unique and multiple environments.
The population must be composed of crosses between a set of at
least three parents (e.g. factorial design, 'diallel', or nested
association mapping). The functions cover data processing,
QTL detection, and results visualization. The implemented methodology
is described in Garin, Wimmer, Mezmouk, Malosetti and van Eeuwijk (2017)
<doi:10.1007/s00122-017-2923-3>, in Garin, Malosetti
and van Eeuwijk (2020) <doi: 10.1007/s00122-020-03621-0>,
and in Garin, Diallo, Tekete, Thera, ..., and Rami (2024) <doi: 10.1093/genetics/iyae003>.

Vincent Garin

mppR

Multi-Parent Population QTL Analysis

Valentin Wimmer

Dietrich Borchardt

Fred van Eeuwijk

Marcos Malosetti

design_connectivity function

<dl><dt>par_per_cross</dt>
<dd>Three columns <code>character matrix</code> specifying :
1) the cross indicators ; 2) the parents 1 identifiers of the crosses;
3) the parents 2 identifiers of the crosses.</dd>
<dt>plot_des</dt>
<dd><code>Logical</code> value indicating if connected part of the
design should be plotted. Default = TRUE.</dd>
<dt>output_loc</dt>
<dd>Path where the plot of the design will be saved if the
argument is given. Default = NULL.</dd></dl>

Arguments

Author

Connected parts of a MPP design — design_connectivity

<dl>

<dt>par_per_cross</dt>
<dd>Three columns <code>character matrix</code> specifying :
1) the cross indicators ; 2) the parents 1 identifiers of the crosses;
3) the parents 2 identifiers of the crosses.</dd>


<dt>plot_des</dt>
<dd><code>Logical</code> value indicating if connected part of the
design should be plotted. Default = TRUE.</dd>


<dt>output_loc</dt>
<dd>Path where the plot of the design will be saved if the
argument is given. Default = NULL.</dd>

</dl>

design_connectivity: Connected parts of a MPP design

Description

Usage

Value

Arguments

Author

References

Examples