calcA

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 

calcA function

<dl><dt>alleles</dt>
<dd>a matrix with {V1 ... Vn, id, parent} providing the alleles
an animal received during each simulation.
The first n columns provide the alleles; the final two columns provide the
animal ID and the parent the allele came from.</dd>
<dt>threshold</dt>
<dd>an integer indicating the maximum number of copies of an
allele that can be present in the population for it to be considered rare.
Default is 1.</dd>
<dt>byID</dt>
<dd>logical variable of length 1 that is passed through to
eventually be used by <code>alleleFreq()</code>, which calculates the count of each
allele in the provided vector. If <code>byID</code> is TRUE and ids are provided,
the function will only count the unique alleles for an individual
(homozygous alleles will be counted as 1).</dd></dl>

Arguments

Count each individual's rare alleles per simulation — calcA

<dl>

<dt>alleles</dt>
<dd>a matrix with {V1 ... Vn, id, parent} providing the alleles
an animal received during each simulation.
The first n columns provide the alleles; the final two columns provide the
animal ID and the parent the allele came from.</dd>


<dt>threshold</dt>
<dd>an integer indicating the maximum number of copies of an
allele that can be present in the population for it to be considered rare.
Default is 1.</dd>


<dt>byID</dt>
<dd>logical variable of length 1 that is passed through to
eventually be used by <code>alleleFreq()</code>, which calculates the count of each
allele in the provided vector. If <code>byID</code> is TRUE and ids are provided,
the function will only count the unique alleles for an individual
(homozygous alleles will be counted as 1).</dd>

</dl>

Count each individual's rare alleles per simulation

calcA: Count each individual's rare alleles per simulation

Description

Usage

Value

Arguments

References

See Also

Examples