calcGameticLD: Calculate the gametic LD matrix for a single parent

In wolfemd/genomicMateSelectR: Genomic Mate Selection

Calculate the gametic LD matrix for a single parent

Description

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).

Usage

calcGameticLD(parentGID, recombFreqMat, haploMat)

Arguments

parentGID	string, the GID of an individual. Needs to correspond to renames in haploMat
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 gametes

See Also

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

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