AlphaSimR (version 0.10.0)

SimParam_restrSegSites: Restrict segregating sites

Description

Sets restrictions on which segregating sites can serve as SNP and/or QTL.

Arguments

maxQtl

the maximum number of segSites for QTLs. Can be a single value or a vector values for each chromosome.

maxSnp

the maximum number of segSites for SNPs. Can be a single value or a vector values for each chromosome.

overlap

should SNP and QTL sites be allowed to overlap.

minSnpFreq

minimum allowable frequency for SNP loci. No minimum SNP frequency is used if value is NULL.

force

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

Usage

SP$restrSegSites(maxQtl = 0, maxSnp = 0, snpQtlOverlap = FALSE, minSnpFreq = NULL, force = FALSE)

Examples

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

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$restrSegSites(maxQtl=5, maxSnp=5)

# }