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

Source: R/predCrossVar_frequentist_univar.R

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

predCrossVarAD(
  sireID,
  damID,
  addEffects,
  domEffects,
  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.
domEffects

column matrix of _dominance_ 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).