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.
genoVarCovarMatFunc(Z)column-centered matrix of SNP dosages. Assumes SNPs in Z were originally coded 0, 1, 2 were column centered.
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
Other helper:
backsolveSNPeff(),
centerDosage(),
crosses2predict(),
dose2domDevGenotypic(),
dose2domDev(),
effectsArray2list(),
genmap2recombfreq(),
getAF(),
getMAF(),
getPropHom(),
intensity(),
kinship(),
maf_filter(),
quadform(),
remove_invariant()