ped1Alleles

ped1Alleles is a dataframe created by the geneDrop function

datasets

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 

ped1Alleles function

A dataframe with 554 rows and 6 variables<dl>
<dt>V1</dt>
<dd>alleles assigned to the parents of the animals identified in
the <code>id</code> column during iteration 1 of gene dropping performed by
<code>geneDrop</code>.</dd><dt>V2</dt>
<dd>alleles assigned to the parents of the animals identified in
the <code>id</code> column during iteration 1 of gene dropping performed by
<code>geneDrop</code>.</dd><dt>V3</dt>
<dd>alleles assigned to the parents of the animals identified in
the <code>id</code> column during iteration 1 of gene dropping performed by
<code>geneDrop</code>.</dd><dt>V4</dt>
<dd>alleles assigned to the parents of the animals identified in
the <code>id</code> column during iteration 1 of gene dropping performed by
<code>geneDrop</code>.</dd><dt>id</dt>
<dd>character vector of animal IDs provided to the gene dropping
function <code>geneDrop</code>.</dd><dt>parent</dt>
<dd>the parent type ("sire" or "dam") of the parent who supplied
the alleles as assigned during each of the 4 gene dropping iterations
performed by <code>geneDrop</code>.</dd>
</dl>

Format

ped1Alleles is a dataframe created by the geneDrop function — ped1Alleles

A dataframe with 554 rows and 6 variables<dl>
<dt>V1</dt>
<dd>alleles assigned to the parents of the animals identified in
the <code>id</code> column during iteration 1 of gene dropping performed by
<code>geneDrop</code>.</dd>

<dt>V2</dt>
<dd>alleles assigned to the parents of the animals identified in
the <code>id</code> column during iteration 1 of gene dropping performed by
<code>geneDrop</code>.</dd>

<dt>V3</dt>
<dd>alleles assigned to the parents of the animals identified in
the <code>id</code> column during iteration 1 of gene dropping performed by
<code>geneDrop</code>.</dd>

<dt>V4</dt>
<dd>alleles assigned to the parents of the animals identified in
the <code>id</code> column during iteration 1 of gene dropping performed by
<code>geneDrop</code>.</dd>

<dt>id</dt>
<dd>character vector of animal IDs provided to the gene dropping
function <code>geneDrop</code>.</dd>

<dt>parent</dt>
<dd>the parent type ("sire" or "dam") of the parent who supplied
the alleles as assigned during each of the 4 gene dropping iterations
performed by <code>geneDrop</code>.</dd>


</dl>

ped1Alleles: ped1Alleles is a dataframe created by the geneDrop function

Description

Usage

Arguments

Format