readKinshipOverrides

Reads an outside-information kinship override table from a
user-supplied file into a data frame for <code>checkKinshipOverrides</code>
and <code>reportGV</code>. The expected long form is the output of
<code>kinMatrix2LongForm</code>: columns <code>id1</code>, <code>id2</code>, and
<code>kinship</code>, with a header row, so a user can export the current matrix,
edit a few rows, and feed it back. Excel (<code>.xls</code>/<code>.xlsx</code>) and
delimited text (<code>.csv</code>/<code>.txt</code>) files are both accepted, mirroring
<code>getGenotypes</code>.

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' 'mulatta')".
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 

readKinshipOverrides function

<dl><dt>fileName</dt>
<dd>character vector of length one; path to the override file
(typically the temporary <code>datapath</code> from a Shiny file upload).</dd>
<dt>sep</dt>
<dd>column separator for delimited text files (default <code>","</code>).</dd></dl>

Arguments

Read a kinship overrides table from a file — readKinshipOverrides

<dl>

<dt>fileName</dt>
<dd>character vector of length one; path to the override file
(typically the temporary <code>datapath</code> from a Shiny file upload).</dd>


<dt>sep</dt>
<dd>column separator for delimited text files (default <code>","</code>).</dd>

</dl>

readKinshipOverrides: Read a kinship overrides table from a file

Description

Usage

Value

Arguments

Details

Examples