get_counts_single_parent

The conditional probability of a genotype at locus \(k+1\) given the genotype at locus
\(k\) is ...

internal

Construction of genetic maps in autopolyploid full-sib populations.
Uses pairwise recombination fraction estimation as the first
source of information to sequentially position allelic variants
in specific homologous chromosomes. For situations where pairwise
analysis has limited power, the algorithm relies on the multilocus
likelihood obtained through a hidden Markov model (HMM).
For more detail, please see Mollinari and Garcia (2019)
<doi:10.1534/g3.119.400378> and Mollinari et al. (2020)
<doi:10.1534/g3.119.400620>.

Marcelo Mollinari

mappoly

Genetic Linkage Maps in Autopolyploids

Gabriel Gesteira

Cristiane Taniguti

Jeekin Lau

Oscar Riera-Lizarazu

Guilhereme Pereira

Augusto Garcia

Zhao-Bang Zeng

Katharine Preedy

Robert Gentleman

Ross Ihaka

R Foundation 

R-core 

get_counts_single_parent function

<dl><dt>ploidy</dt>
<dd>Ploidy level</dd>
<dt>gen.par.mk1</dt>
<dd>Genotype of marker mk1 (vector \(x \in 0, \cdots, m\))</dd>
<dt>gen.par.mk2</dt>
<dd>Genotype of marker mk2 (vector \(x \in 0, \cdots, m\))</dd>
<dt>gen.prog.mk1</dt>
<dd>Dose of marker mk1 on progeny</dd>
<dt>gen.prog.mk2</dt>
<dd>Dose of marker mk2 on progeny</dd></dl>

Arguments

Counts for recombinant classes in a polyploid parent. — get_counts_single_parent

<dl>

<dt>ploidy</dt>
<dd>Ploidy level</dd>


<dt>gen.par.mk1</dt>
<dd>Genotype of marker mk1 (vector \(x \in 0, \cdots, m\))</dd>


<dt>gen.par.mk2</dt>
<dd>Genotype of marker mk2 (vector \(x \in 0, \cdots, m\))</dd>


<dt>gen.prog.mk1</dt>
<dd>Dose of marker mk1 on progeny</dd>


<dt>gen.prog.mk2</dt>
<dd>Dose of marker mk2 on progeny</dd>

</dl>

Counts for recombinant classes in a polyploid parent.

get_counts_single_parent: Counts for recombinant classes in a polyploid parent.

Description

Usage

Value

Arguments