check_marker_assignment

A marker assignment matrix for parent 1 with markernames as rownames and at least containing the column <code>"Assigned_LG"</code>; the output of <code><a rd-options="" href="/link/homologue_lg_assignment?package=polymapR&version=1.1.2" data-mini-rdoc="polymapR::homologue_lg_assignment">homologue_lg_assignment</a></code>.

marker_assignment.P1

A marker assignment matrix for parent 2 with markernames as rownames and at least containing the column <code>"Assigned_LG"</code>; the output of <code><a rd-options="" href="/link/homologue_lg_assignment?package=polymapR&version=1.1.2" data-mini-rdoc="polymapR::homologue_lg_assignment">homologue_lg_assignment</a></code>.

marker_assignment.P2

Character string specifying the log filename to which standard output should be written. If NULL (by default) log is send to stdout.

Should messages be sent to stdout or log?

verbose

Function to ensure there is consistent marker assignment to chromosomal linkage groups
for biparental markers

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. (submitted, 2020).

Peter Bourke

polymapR

Linkage Analysis in Outcrossing Polyploids

Geert van Geest

Roeland Voorrips

Yanlin Liao

check_marker_assignment function

<dl><dt>marker_assignment.P1</dt>
<dd>A marker assignment matrix for parent 1 with markernames as rownames and at least containing the column <code>"Assigned_LG"</code>; the output of <code>homologue_lg_assignment</code>.</dd>
<dt>marker_assignment.P2</dt>
<dd>A marker assignment matrix for parent 2 with markernames as rownames and at least containing the column <code>"Assigned_LG"</code>; the output of <code>homologue_lg_assignment</code>.</dd>
<dt>log</dt>
<dd>Character string specifying the log filename to which standard output should be written. If NULL (by default) log is send to stdout.</dd>
<dt>verbose</dt>
<dd>Should messages be sent to stdout or log?</dd></dl>

Arguments

Check for consistent marker assignment between both parents — check_marker_assignment

<dl>

<dt>marker_assignment.P1</dt>
<dd>A marker assignment matrix for parent 1 with markernames as rownames and at least containing the column <code>"Assigned_LG"</code>; the output of <code>homologue_lg_assignment</code>.</dd>


<dt>marker_assignment.P2</dt>
<dd>A marker assignment matrix for parent 2 with markernames as rownames and at least containing the column <code>"Assigned_LG"</code>; the output of <code>homologue_lg_assignment</code>.</dd>


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


<dt>verbose</dt>
<dd>Should messages be sent to stdout or log?</dd>

</dl>

check_marker_assignment: Check for consistent marker assignment between both parents

Description

Usage

Value

Arguments

Examples