predCrossVarA: Single trait prediction of the additive genetic variance in a...

In wolfemd/predCrossVar: Prediction of family genomic variances and covariances

Description

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

Usage

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.
...

Details

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

Value

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

wolfemd/predCrossVar documentation built on Dec. 21, 2020, 10:14 a.m.