checkKinshipOverrides

Checks the structure and domain of an outside-information kinship override
table. The table supplies pairwise kinship coefficients
(<code>id1</code>, <code>id2</code>, <code>kinship</code>) that
<code>applyKinshipOverrides</code> writes into a computed kinship matrix,
replacing the pedigree-derived value for those pairs. It mirrors
<code>checkGenotypeFile</code>: it <code><a href="/link/stop()?package=nprcgenekeepr&version=2.0.0" data-mini-rdoc="nprcgenekeepr::stop()">stop()</a></code>s on structural or domain
errors and returns the (id-coerced) table when the input is acceptable.

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 

checkKinshipOverrides function

<dl><dt>overrides</dt>
<dd>data.frame with id columns <code>id1</code> and <code>id2</code> and a
numeric <code>kinship</code> column; each row is one off-diagonal pair. Any extra
columns are ignored.</dd></dl>

Arguments

Checks the structure and domain of an outside-information kinship override
table. The table supplies pairwise kinship coefficients
(<code>id1</code>, <code>id2</code>, <code>kinship</code>) that
<code>applyKinshipOverrides</code> writes into a computed kinship matrix,
replacing the pedigree-derived value for those pairs. It mirrors
<code>checkGenotypeFile</code>: it <code><a href='https://rdrr.io/r/base/stop.html'>stop()</a></code>s on structural or domain
errors and returns the (id-coerced) table when the input is acceptable.

Validate a kinship overrides table — checkKinshipOverrides

<dl>

<dt>overrides</dt>
<dd>data.frame with id columns <code>id1</code> and <code>id2</code> and a
numeric <code>kinship</code> column; each row is one off-diagonal pair. Any extra
columns are ignored.</dd>

</dl>

checkKinshipOverrides: Validate a kinship overrides table

Description

Usage

Value

Arguments

Details

Examples