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nadiv (version 2.7)

Functions to construct non-additive genetic relatedness matrices

Description

Constructs non-additive genetic relationship matrices from a pedigree. These and their inverses can be passed to a linear mixed effect model, known as the 'animal model'.

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Version

Install

install.packages('nadiv')

Monthly Downloads

897

Version

2.7

License

GPL (>= 2)

Maintainer

Matthew Wolak

Last Published

December 18th, 2011

Functions in nadiv (2.7)

vchoose

Helper function for another internal function in makeDsim

makeDomEpi

Creates the additive by dominance and dominance by dominance epistatic genetic relationship matrices

makeDsim

Creates the dominance genetic relationship matrix through simulation

Mrode2

Pedigree from Table 2.1 of Mrode (2005)

makeAA

Creates the additive by additive epistatic genetic relationship matrix

FindDFC

Finds the double first cousins in a pedigree

genAssign

Generation assignment

sm2list

Converts a sparse matrix into a three column format.

DFC

Indicates Double First Cousins

warcolak

Pedigree and phenotypic values for a mythical half-sib population of Warcolaks

choose

Internal function for makeDsim

makeA

Creates the additive genetic relationship matrix

IBD

Identical by descent

SEfun

Estimate of the standard error for a simulated coefficient of fraternity

IBD2

Identity by descent helper function

aiFun

Sampling (co)variances and correlations of random terms

Mrode9

Pedigree, adapted from example 9.1 of Mrode (2005)

makeD

Creates the dominance genetic realationship matrix

numPed

Creates a numeric form of a pedigree

nadiv-package

Functions to create non-additive relationship matrices and their inverses