assignAlleles

Provides genetic tools for colony management and is a derivation
of the work in Amanda Vinson and Michael J Raboin (2015)
<https://pmc.ncbi.nlm.nih.gov/articles/PMC4671785/> "A Practical
Approach for Designing Breeding Groups to Maximize Genetic Diversity in a
Large Colony of Captive Rhesus Macaques ('Macaca' 'mulatto')".
It provides a 'Shiny' application with an exposed API.
The application supports five groups of functions:
(1) Quality control of studbooks contained in text files or 'Excel'
workbooks and of pedigrees within 'LabKey' Electronic Health Records
(EHR);
(2) Creation of pedigrees from a list of animals using the 'LabKey' EHR
integration;
(3) Creation and display of an age by sex pyramid plot of the living
animals within the designated pedigree;
(4) Generation of genetic value analysis reports; and
(5) Creation of potential breeding groups with and without proscribed sex
ratios and defined maximum kinships.

R. Mark Sharp

nprcgenekeepr

Genetic Tools for Colony Management

Michael Raboin

Terry Therneau

Amanda Vinson

Matthew Schultz

Southwest National Primate Research Center NIH grant P51 RR13986 

Oregon National Primate Research Center grant P51 OD011092 

assignAlleles function

<dl><dt>alleles</dt>
<dd>a list with a list <code>alleles$alleles</code>, which is a list
of list containing the alleles for each individual's sire and dam that have
been assigned thus far and <code>alleles$counter</code> that is the counter used
to track the lists of<code>alleles$alleles</code>.</dd>
<dt>parentType</dt>
<dd>character vector of length one with value of
<code>"sire"</code> or <code>"dam"</code>.</dd>
<dt>parent</dt>
<dd>either <code>ped[id, "sire"]</code> or <code>ped[id, "dam"]</code>.</dd>
<dt>id</dt>
<dd>character vector of length one containing the animal ID</dd>
<dt>n</dt>
<dd>integer indicating the number of iterations to simulate.
Default is 5000.</dd></dl>

Arguments

Assign parent alleles randomly — assignAlleles

<dl>

<dt>alleles</dt>
<dd>a list with a list <code>alleles$alleles</code>, which is a list
of list containing the alleles for each individual's sire and dam that have
been assigned thus far and <code>alleles$counter</code> that is the counter used
to track the lists of<code>alleles$alleles</code>.</dd>


<dt>parentType</dt>
<dd>character vector of length one with value of
<code>"sire"</code> or <code>"dam"</code>.</dd>


<dt>parent</dt>
<dd>either <code>ped[id, "sire"]</code> or <code>ped[id, "dam"]</code>.</dd>


<dt>id</dt>
<dd>character vector of length one containing the animal ID</dd>


<dt>n</dt>
<dd>integer indicating the number of iterations to simulate.
Default is 5000.</dd>

</dl>

Assign parent alleles randomly

assignAlleles: Assign parent alleles randomly

Description

Usage

Value

Arguments

Examples