segMaker

Function to generate list of segregation types for the <code>exploreQTL</code> function

Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in
autopolyploid bi-parental F1 populations.
For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated.
Significance thresholds, exploring QTL allele effects and visualising results are provided.
For more background and to reference the package see <doi:10.1093/bioinformatics/btab574>.

Peter Bourke

polyqtlR

QTL Analysis in Autopolyploid Bi-Parental F1 Populations

Christine Hackett

Chris Maliepaard

Geert van Geest

Roeland Voorrips

Johan Willemsen

segMaker function

<dl><dt>ploidy</dt>
<dd>The ploidy of the population. Currently assumed to be an even number for this function.</dd>
<dt>segtypes</dt>
<dd>List of QTL segregation types to consider,
so e.g. c(1,0) would mean all possible simplex x nulliplex QTL (ie. 4 QTL, on each of homologues 1 - 4 of parent 1).
Note that symmetrical QTL types that cannot be distinguished are not automatically removed and need to be manually identified.
If this is an issue, use the inbuilt list for tetraploids provided with the package to search the full model space.
Such an inbuilt list is currently only available for tetraploids, and is available from the <code>exploreQTL</code> function.</dd>
<dt>modes</dt>
<dd>Character vector of modes of QTL action to consider, with options "a" for "additive" and "d" for dominant QTL action.</dd></dl>

Arguments

Create a list of possible QTL segregation types — segMaker

<dl>

<dt>ploidy</dt>
<dd>The ploidy of the population. Currently assumed to be an even number for this function.</dd>


<dt>segtypes</dt>
<dd>List of QTL segregation types to consider,
so e.g. c(1,0) would mean all possible simplex x nulliplex QTL (ie. 4 QTL, on each of homologues 1 - 4 of parent 1).
Note that symmetrical QTL types that cannot be distinguished are not automatically removed and need to be manually identified.
If this is an issue, use the inbuilt list for tetraploids provided with the package to search the full model space.
Such an inbuilt list is currently only available for tetraploids, and is available from the <code>exploreQTL</code> function.</dd>


<dt>modes</dt>
<dd>Character vector of modes of QTL action to consider, with options "a" for "additive" and "d" for dominant QTL action.</dd>

</dl>

segMaker: Create a list of possible QTL segregation types

Description

Usage

Arguments