Function to compute gametic LD matrix for a single parent. Uses a matrix of recombination frequencies and the supplied haplotypes of the parent as in Bijma et al. 2020 and Lehermeier et al. 2017b (and others).
calcGameticLD(parentGID, recombFreqMat, haploMat)string, the GID of an individual. Needs to correspond to renames in haploMat
a square symmetric matrix with values = (1-2*c1), where c1=matrix of expected recomb. frequencies. The choice to do 1-2c1 outside the function was made for computation efficiency; every operation on a big matrix takes time.
matrix of phased haplotypes, 2 rows per sample, cols = loci, 0,1, rownames assumed to contain GIDs with a suffix, separated by "_" to distinguish haplotypes
Potentially really large matrix representing the LD between loci in gametes
Columns of haploMat and row/cols of recombFreqMat should be in same order. May be worth computing in an R session using multi-threaded BLAS.
Other predCrossVar:
calcCrossLD(),
predCrossMeans(),
predCrossVars()