AlphaSimR (version 0.11.0)

SimParam_setMeiosis: Set meiosis parameters

Description

Changes parameters defining the amount of crossover interference, the gender specific recombination ratio, or the probability of quadrivalent pairing in autopolyploids. Parameters are only changed if specified by the user. The default values for the parameters are indicated in descriptions below.

Arguments

v

the crossover interference parameter for a gamma model of recombination. A value of 1 indicates no crossover interference (e.g. Haldane mapping function). A value of 2.65 approximates the degree of crossover interference implied by the Kosambi mapping function. (default is 1)

ratio

relative ratio of recombination in females compared to males. A value of 2 indicate twice as much recombination in females and a value of 1/2 would indicate half as much recombinations. The value must be greater than 0. (default is 1)

quadProb

the probability of quadrivalent pairing in an autopolyploid. A value of 2/3 equals the probability expected under random pairing of telomeres in a tetraploid. (default is 0)

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Usage

SP$setMeiosis(v = NULL, ratio = NULL, quadProb = NULL, force = FALSE)

Examples

# NOT RUN {
#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$setMeiosis(ratio=2) #Twice as much recombination in females

# }