Generation of the haplotype crossing matrix associated to a Genome
object.
haploCrossMatrix(genomeObj)An haplotype crossing matrix.
a Genome object
Ehouarn Le Faou
A crossover matrix is a square matrix of size equal to the number of haplotypes. It describes for each combination of two gametic haplotypes the genotype index resulting from their syngamy. In the general case it is not a symmetrical matrix (it is if a single haploid locus with a single allele is defined), because the transmission of haploid loci is only maternal, therefore non-symmetrical as is the transmission of diploid loci. It is therefore necessary to enter the haplotype frequencies of male gametes in the columns and the haplotype frequencies of female gametes in the rows during the calculations (this is done in the simulations).