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pedigreeTools (version 0.2)

Versatile Functions for Working with Pedigrees

Description

Tools to sort, edit and prune pedigrees and to extract the inbreeding coefficients and the relationship matrix (includes code for pedigrees from self-pollinated species). The use of pedigree data is central to genetics research within the animal and plant breeding communities to predict breeding values. The relationship matrix between the individuals can be derived from pedigree structure ('Vazquez et al., 2010') .

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Version

Install

install.packages('pedigreeTools')

Monthly Downloads

233

Version

0.2

License

GPL-3

Issues

5

Pull Requests

2

Stars

14

Forks

8

Maintainer

Paulino Rodriguez

Last Published

August 15th, 2023

Functions in pedigreeTools (0.2)

getTInv

Inverse gene flow from a pedigree
pedigreeTools-package

pedigreeTools: Versatile Functions for Working with Pedigrees
pedigree

Constructor for pedigree objects
pedigree-class

Pedigree class
getGenAncestors

Counts number of generations of ancestors for one subject. Use recursion.
getA

Additive relationship matrix
getAInv

Inverse of the additive relationship matrix
getT

Gene flow from a pedigree
Dmat

Mendelian sampling variance
editPed

Edits a disordered or incomplete pedigree
relfactorInv

Inverse relationship factor from a pedigree
prunePed

Subsets a pedigree for a specified vector of individuals up to a specified number of previous generations using recursion.
inbreeding

Inbreeding coefficients from a pedigree
relfactor

Relationship factor from a pedigree
ped2DF

Convert a pedigree to a data frame
getASelfing

Extends the pedigree according to number of selfing cycles and also optionally computes the Additive Relationship Matrix for that pedigree.
getASubset

Subset of additive relationship matrix