getProbandPedigree

Filters a pedigree down to only the ancestors of the provided group,
removing unnecessary individuals from the studbook. This version builds
the pedigree back in time starting from a group of probands. This will
include all ancestors of the probands, even ones that might be
uninformative.

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 

getProbandPedigree function

<dl><dt>probands</dt>
<dd>a character vector with the list of animals whose ancestors
should be included in the final pedigree.</dd>
<dt>ped</dt>
<dd>datatable that is the <code>Pedigree</code>. It contains pedigree
information. The fields <code>sire</code> and <code>dam</code> are required.</dd></dl>

Arguments

Gets pedigree to ancestors of provided group leaving uninformative ancestors. — getProbandPedigree

<dl>

<dt>probands</dt>
<dd>a character vector with the list of animals whose ancestors
should be included in the final pedigree.</dd>


<dt>ped</dt>
<dd>datatable that is the <code>Pedigree</code>. It contains pedigree
information. The fields <code>sire</code> and <code>dam</code> are required.</dd>

</dl>

getProbandPedigree: Gets pedigree to ancestors of provided group leaving uninformative ancestors.

Description

Usage

Value

Arguments

Examples