newMapPop {AlphaSimR} | R Documentation |
Creates a new MapPop-class
from user supplied
genetic maps and haplotypes.
newMapPop(genMap, haplotypes, inbred = FALSE, ploidy = 2L)
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 |
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
an object of MapPop-class
# 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)