generate_all_link_phase_elim_equivalent

Generate all possible linkage phases in matrix form given the dose
and the number of shared alleles between a inserted marker and a
pre-computed linkage configuration.

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 

generate_all_link_phase_elim_equivalent function

<dl><dt>X</dt>
<dd>a list of matrices whose columns represent homologous
chromosomes and the rows represent markers. Each element of the
list represents a linkage phase configuration.</dd>
<dt>d</dt>
<dd>the dosage of the inserted marker</dd>
<dt>sh</dt>
<dd>the number of shared alleles between k1 (marker already
present on the sequence) and k2 (the inserted marker)</dd>
<dt>ploidy</dt>
<dd>the ploidy level</dd>
<dt>k1</dt>
<dd>marker already present on the sequence</dd>
<dt>k2</dt>
<dd>inserted marker</dd></dl>

Arguments

Generate all possible linkage phases in matrix form given the dose
and the number of shared alleles between a inserted marker and a
pre-computed linkage configuration. — generate_all_link_phase_elim_equivalent

<dl>

<dt>X</dt>
<dd>a list of matrices whose columns represent homologous
chromosomes and the rows represent markers. Each element of the
list represents a linkage phase configuration.</dd>


<dt>d</dt>
<dd>the dosage of the inserted marker</dd>


<dt>sh</dt>
<dd>the number of shared alleles between k1 (marker already
present on the sequence) and k2 (the inserted marker)</dd>


<dt>ploidy</dt>
<dd>the ploidy level</dd>


<dt>k1</dt>
<dd>marker already present on the sequence</dd>


<dt>k2</dt>
<dd>inserted marker</dd>

</dl>

Generate all possible linkage phases in matrix form given the dose
and the number of shared alleles between a inserted marker and a
pre-computed linkage configuration.

generate_all_link_phase_elim_equivalent: Generate all possible linkage phases in matrix form given the dose and the number of shared alleles between a inserted marker and a pre-computed linkage configuration.

Description

Usage

Value

Arguments