Single trait prediction of the additive genetic variance in a one cross

Source: R/predCrossVar_frequentist_univar.R

Function to predict the additive genetic variances among full-siblings of a single, user-specified cross.

predCrossVarA(sireID, damID, addEffects, haploMat, recombFreqMat, ...)

Arguments

sireID

string, Sire genotype ID. Needs to correspond to renames in haploMat
damID

string, Dam genotype ID. Needs to correspond to renames in haploMat
addEffects

column matrix of _additive_ SNP effects estimate with rownames == SNP_IDs and matches the order of related SNP matrices.
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
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.
...

Value

a tibble with values for predicted add/dom variances as well as compute time and memory usage stats

Details

SNP_IDs must match: names(addEffects)==names(domEffects)==colnames(haploMat)==rownames(recombFreqMat)==colnames(recombFreqMat).