newMapPop {AlphaSimR}

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 the organism

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. The number of rows must match the number of individuals times the ploidy if using inbred=FALSE. If using inbred=TRUE, the number of rows must equal the number of individuals. The haplotypes can be stored as numeric, integer or raw. The underlying C++ function will use raw.

Value

an object of MapPop-class

Examples

# 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)