AlphaSimR (version 0.10.0)

newMapPop: New MapPop

Description

Creates a new MapPop-class from user supplied genetic maps and haplotypes.

Usage

newMapPop(genMap, haplotypes, inbred = FALSE, ploidy = 2L)

Arguments

genMap

a list of genetic maps

haplotypes

a list of matrices or data.frames that can be coerced to matrices. See details.

inbred

are individuals fully inbred

ploidy

ploidy level of organism

Value

an object of MapPop-class

Details

Each item of genMap must be a vector of ordered genetic lengths in Morgans. The first value must be zero. The length of the vector determines the number of segregating sites on the chromosome.

Each item of haplotypes must be coercible to a matrix. The columns of this matrix correspond to segregating sites and their number must match

Examples

# NOT RUN {
# Create genetic map for two chromosomes, each 1 Morgan long
# Each chromosome contains 11 equally spaced segregating sites
genMap = list(seq(0,1,length.out=11),
               seq(0,1,length.out=11))
               
# Create haplotypes for 10 outbred individuals
chr1 = sample(x=0:1,size=20*11,replace=TRUE)
chr1 = matrix(chr1,nrow=20,ncol=11)
chr2 = sample(x=0:1,size=20*11,replace=TRUE)
chr2 = matrix(chr2,nrow=20,ncol=11)
haplotypes = list(chr1,chr2)

founderPop = newMapPop(genMap=genMap,haplotypes=haplotypes)

# }