concatenate_new_marker

Inserts a new marker at the end of the sequence, taking into account
the two-point information

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 

concatenate_new_marker function

<dl><dt>X</dt>
<dd>a list of matrices whose columns represent homologous
chromosomes and the rows represent markers</dd>
<dt>d</dt>
<dd>the dosage of the inserted marker</dd>
<dt>sh</dt>
<dd>a list of shared alleles between all markers in the sequence</dd>
<dt>seq.num</dt>
<dd>a vector of integers containing the number of each marker in the raw data file</dd>
<dt>ploidy</dt>
<dd>the ploidy level</dd>
<dt>mrk</dt>
<dd>the marker to be inserted</dd></dl>

Arguments

Concatenate new marker — concatenate_new_marker

<dl>

<dt>X</dt>
<dd>a list of matrices whose columns represent homologous
chromosomes and the rows represent markers</dd>


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


<dt>sh</dt>
<dd>a list of shared alleles between all markers in the sequence</dd>


<dt>seq.num</dt>
<dd>a vector of integers containing the number of each marker in the raw data file</dd>


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


<dt>mrk</dt>
<dd>the marker to be inserted</dd>

</dl>

Concatenate new marker

concatenate_new_marker: Concatenate new marker

Description

Usage

Value

Arguments