Single-trait prediction of the additive genetic variance for multiple crosses

Source: R/predCrossVar_frequentist_univar.R

Wraps around `predCrossVarA()` to predict multiple crosses. Option for parallelizing prediction across families. If outprefix and outpath are supplied, writes output to disk so impatient users can see results.

runCrossVarPredsA(
  outprefix = NULL,
  outpath = NULL,
  ped,
  addEffects,
  haploMat,
  recombFreqMat,
  ncores = 1,
  ...
)

Arguments

ped

pedigree data.frame, cols: sireID, damID. sireID and damID must both be in the haploMat.
addEffects

vector of _additive_ SNP effects estimate. Ideally vector is named with 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.
ncores

If ncores set > 1 parallelizes across families, but beware it is memory intensive and options(future.globals.maxSize=___) may need to be adjusted.
...

Value