genoVarCovarMatFunc: Compute the LD matrix from dosages

In wolfemd/genomicMateSelectR: Genomic Mate Selection

Compute the LD matrix from dosages

Description

Compute the p_{SNP} \times p_{SNP} variance-covariance matrix of SNP dosages. This is an estimator of the LD between loci within a given population.

Usage

genoVarCovarMatFunc(Z)

Arguments

Z	column-centered matrix of SNP dosages. Assumes SNPs in Z were originally coded 0, 1, 2 were column centered.

Value

NOTE: this matrix is going to be big in practice. The p_{SNP} \times p_{SNP} variance-covariance matrix of SNP dosages. may be worth computing in an R session using multi-threaded BLAS

See Also

Other helper: backsolveSNPeff(), centerDosage(), crosses2predict(), dose2domDevGenotypic(), dose2domDev(), effectsArray2list(), genmap2recombfreq(), getAF(), getMAF(), getPropHom(), intensity(), kinship(), maf_filter(), quadform(), remove_invariant()

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