Calculate the cross LD matrix based on both parents

Wraps the calcGameticLD function. CrossLD = sireLD + damLD.

calcCrossLD(sireID, damID, recombFreqMat, haploMat)

Arguments

sireID

string, Male parent genotype ID.

damID

string, Female parent genotype ID.

recombFreqMat

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.

haploMat

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

Value

Potentially really large matrix representing the LD between loci in the cross

Details

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.

See also

Other predCrossVar: calcGameticLD(), predCrossMeans(), predCrossVars()