nprcgenekeepr-package: Genetic Management Functions

In rmsharp/nprcmanager: Genetic Tools for Colony Management

Genetic Management Functions

Description

Primary Data Structure — Pedigree

Contains studbook information for a number of individuals. ASSUME: All IDs listed in the sire or dam columns must have a row entry in the id column

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.

Author(s)

Maintainer: R. Mark Sharp [e-mail] (ORCID) [copyright holder, data contributor]

Authors:

• Michael Raboin

• Terry Therneau

• Amanda Vinson [data contributor]

• Matthew Schultz (ORCID)

Other contributors:

• Southwest National Primate Research Center NIH grant P51 RR13986 [funder]

• Oregon National Primate Research Center grant P51 OD011092 [funder]

See Also

getIncludeColumns to get set of columns that can be used in a pedigree file

A Pedigree is a data frame within the R environment with the following possible columns:

• {id} {– character vector with unique identifier for an individual}

• {sire} {– character vector with unique identifier for an individual's father (NA if unknown).}

• {dam} {– character vector with unique identifier for an individual's mother (NA if unknown).}

• {sex} {– factor {levels: "M", "F", "U"} Sex specifier for an individual}

• {gen} {– integer vector with the generation number of the individual}

• {birth} {– Date or NA (optional) with the individual's birth date}

• {exit} {– Date or NA (optional) with the individual's exit date (death, or departure if applicable)}

• {ancestry} {– character vector or NA (optional) that indicates the geographic population to which the individual belongs.}

• {age} {– numeric or NA (optional) indicating the individual's current age or age at exit.}

• {population} {– logical (optional) Is the id part of the extant population?}

• {origin} {– character vector or NA (optional) that indicates the name of the facility that the individual was imported from if other than local.NA indicates the individual was not imported.}

Pedigree File Testing Functions

• {qcStudbook} {— Main pedigree curation function that performs basic quality control on pedigree information}

• {fixColumnNames} {— Changes original column names and into standardized names.}

• {checkRequiredCols} {— Examines column names, cols, to see if all required column names are present.}

• {correctParentSex} {— Sets sex for animals listed as either a sire or dam.}

• {getDateErrorsAndConvertDatesInPed} {— Converts columns of dates in text form to Date object columns}

• {checkParentAge} {— Check parent ages to be at least minParentAge}

• {removeDuplicates} {— Remove duplicate records from pedigree}

Gene Dropping Function

• {geneDrop} {— Performs a gene drop simulation based on the provided pedigree information}

Genetic Value Analysis Functions

Contains functions to calculate the kinship coefficient and genome uniqueness for animals listed in a Pedigree table.

• {meanKinship} {— Calculates the mean kinship for each animal in a kinship matrix}

• {calcA} {— Calculates a, the number of an individual's alleles that are rare in each simulation.}

• {alleleFreq} {— Calculates the count of each allele in the provided vector.}

• {calcFE} {— Calculates founder equivalents.}

• {calcFG} {— Calculates founder genome equivalents.}

• {calcFEFG} {— Returns founder equivalents FE and FG as elements in a list.}

• {calcGU} {— Calculates genome uniqueness for each ID that is part of the population.}

• {geneDrop} {— Performs a gene drop simulation based on the pedigree information.}

• {chooseAlleles} {— Combines two vectors of alleles by randomly selecting one allele or the other at each position.}

• {calcRetention} {— Calculates allelic retention.}

• {filterKinMatrix} {— Filters a kinship matrix to include only the egos listed in 'ids'}

• {kinship} {— Generates a kinship matrix}

• {reportGV} {— Generates a genetic value report for a provided pedigree.}

Plotting Functions

• {meanKinship} {— Calculates the mean kinship for each animal in a kinship matrix}

Breeding Group Formation Functions

• {meanKinship} {— Calculates the mean kinship for each animal in a kinship matrix}

Useful links:

• https://rmsharp.github.io/nprcgenekeepr/

• https://github.com/rmsharp/nprcgenekeepr

• Report bugs at https://github.com/rmsharp/nprcgenekeepr/issues

rmsharp/nprcmanager documentation built on Feb. 2, 2025, 12:45 a.m.