newMapPop {AlphaSimR} | R Documentation |
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)