add_dup_markers

Often there will be duplicate markers that can be put aside to speed up mapping. These may be added back to the maps afterwards.

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

add_dup_markers function

<dl><dt>maplist</dt>
<dd>A list of maps. Output of MDSMap_from_list.</dd>
<dt>bin_list</dt>
<dd>A list of marker bins containing marker duplicates. One of the list outputs of <code>screen_for_duplicate_markers</code></dd>
<dt>marker_assignments</dt>
<dd>Optional argument to include the marker_assignments (output of <code>check_marker_assignment</code>). If included, marker assignment information will also be copied.</dd></dl>

Arguments

Add back duplicate markers after mapping — add_dup_markers

<dl>

<dt>maplist</dt>
<dd>A list of maps. Output of MDSMap_from_list.</dd>


<dt>bin_list</dt>
<dd>A list of marker bins containing marker duplicates. One of the list outputs of <code>screen_for_duplicate_markers</code></dd>


<dt>marker_assignments</dt>
<dd>Optional argument to include the marker_assignments (output of <code>check_marker_assignment</code>). If included, marker assignment information will also be copied.</dd>

</dl>

add_dup_markers: Add back duplicate markers after mapping

Description

Usage

Value

Arguments