mutate {AlphaSimR}

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)