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pedigreeTools (version 0.3)

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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Install

install.packages('pedigreeTools')

Monthly Downloads

233

Version

0.3

License

GPL-3

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Maintainer

Paulino Rodriguez

Last Published

October 12th, 2024

Functions in pedigreeTools (0.3)

pedigree

Constructor for pedigree objects
pedigreeTools-package

pedigreeTools: Versatile Functions for Working with Pedigrees
getASelfing

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

Mendelian sampling variance
inbreeding

Inbreeding coefficients from a pedigree
getTInv

Inverse gene flow from a pedigree
prunePed

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

Edits a disordered or incomplete pedigree
getA

Additive relationship matrix
getT

Gene flow from a pedigree
getGenAncestors

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

Relationship factor from a pedigree
getASubset

Subset of additive relationship matrix
ped2DF

Convert a pedigree to a data frame
getAInv

Inverse of the additive relationship matrix
pedigree-class

Pedigree class
relfactorInv

Inverse relationship factor from a pedigree