calcCrossLD: Calculate the cross LD matrix based on both parents

In wolfemd/genomicMateSelectR: Genomic Mate Selection

Calculate the cross LD matrix based on both parents

Description

Wraps the calcGameticLD function. CrossLD = sireLD + damLD.

Usage

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

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.

Value

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

See Also

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

wolfemd/genomicMateSelectR documentation built on July 1, 2022, 10:42 p.m.