subPed

Creates a subset of a large pedigree that includes only individuals related with specified individuals in a predefined way.

A framework for the optimization of breeding programs via optimum contribution selection and mate allocation. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees. The methods are described in:\n Wellmann, R., and Pfeiffer, I. (2009) <doi:10.1017/S0016672309000202>.\n Wellmann, R., and Bennewitz, J. (2011) <doi:10.2527/jas.2010-3709>.\n Wellmann, R., Hartwig, S., Bennewitz, J. (2012) <doi:10.1186/1297-9686-44-34>.\n de Cara, M. A. R., Villanueva, B., Toro, M. A., Fernandez, J. (2013) <doi:10.1111/mec.12560>.\n Wellmann, R., Bennewitz, J., Meuwissen, T.H.E. (2014) <doi:10.1017/S0016672314000196>.\n Wellmann, R. (2019) <doi:10.1186/s12859-018-2450-5>.

Robin Wellmann

optiSel

Optimum Contribution Selection and Population Genetics

subPed function

<dl><dt>Pedig</dt>
<dd>Data frame containing the pedigree where the first 3 columns correspond to: Individual ID, Sire, and Dam. More columns can be passed in the <code>Pedig</code> argument including columns named <code>Sex</code>, <code>Breed</code> (with breed names), and <code>Born</code> (with years of birth). Missing parents are coded as NA, 0, or "0".</dd><dt>keep</dt>
<dd>Vector with IDs of individuals. Only these individuals and individuals related with them in a predefined way will be kept in the pedigree.</dd><dt>prevGen</dt>
<dd>Number of previous (ancestral) generations to be included in the pedigree.</dd><dt>succGen</dt>
<dd>Number of succeeding (descendant) generations to be included in the pedigree.</dd></dl>

Arguments

Author

Creates a Subset of a Large Pedigree — subPed

<dl>

<dt>Pedig</dt>
<dd>Data frame containing the pedigree where the first 3 columns correspond to: Individual ID, Sire, and Dam. More columns can be passed in the <code>Pedig</code> argument including columns named <code>Sex</code>, <code>Breed</code> (with breed names), and <code>Born</code> (with years of birth). Missing parents are coded as NA, 0, or "0".</dd>

<dt>keep</dt>
<dd>Vector with IDs of individuals. Only these individuals and individuals related with them in a predefined way will be kept in the pedigree.</dd>

<dt>prevGen</dt>
<dd>Number of previous (ancestral) generations to be included in the pedigree.</dd>

<dt>succGen</dt>
<dd>Number of succeeding (descendant) generations to be included in the pedigree.</dd>

</dl>

subPed: Creates a Subset of a Large Pedigree

Description

Usage

Value

Arguments

Author

Details

Examples