AlphaSimR: mutate – R documentation

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mutate

Add Random Mutations

Description

Adds random mutations to individuals in a population. Note that any existing phenotypes or EBVs are kept. Thus, the user will need to run setPheno and/or setEBV to generate new phenotypes or EBVs that reflect changes introduced by the new mutations.

Usage

mutate(pop, mutRate = 2.5e-08, returnPos = FALSE, simParam = NULL)

Arguments

`pop`	an object of `Pop-class`
`mutRate`	rate of new mutations
`returnPos`	should the positions of mutations be returned
`simParam`	an object of `SimParam`

Value

an object of Pop-class if returnPos=FALSE or a list containing a Pop-class and a data.frame containing the postions of mutations if returnPos=TRUE

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitA(10)

#Create population
pop = newPop(founderPop, simParam=SP)

#Introduce mutations
pop = mutate(pop, simParam=SP)

AlphaSimR

Breeding Program Simulations

v0.13.0

MIT + file LICENSE

Authors

Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>), Gregor Gorjanc [aut] (<https://orcid.org/0000-0001-8008-2787>), John Hickey [aut] (<https://orcid.org/0000-0001-5675-3974>), Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>), David Wilson [ctb]

Initial release

2020-10-20