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nprcgenekeepr (version 1.0.8)

nprcgenekeepr-package: 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

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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.

Arguments

Author

Maintainer: R. Mark Sharp rmsharp@me.com (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: