phenoRegressor.rrBLUP.SNP: SNP-BLUP using rrBLUP library

In GROAN: Genomic Regression Workbench

SNP-BLUP using rrBLUP library

Description

Implementation of SNP-BLUP using rrBLUP library. Not to be exported.

Usage

phenoRegressor.rrBLUP.SNP(phenotypes, genotypes, extraCovariates = NULL, ...)

Arguments

phenotypes	phenotypes, a numeric array (n x 1), missing values are predicted
genotypes	SNP genotypes, one row per phenotype (n), one column per marker (m), values in 0/1/2 for diploids or 0/1/2/...ploidy for polyploids. Can be NULL if covariances is present.
extraCovariates	optional extra covariates set, one row per phenotype (n), one column per covariate (w). If NULL no extra covariates are considered.
...	extra parameters are passed to rrBLUP::mixed.solve

Value

The function returns a list with the following fields:

• predictions : an array of (k) predicted phenotypes

• hyperparams : named vector with the following keys: Vu, Ve, beta, LL

• extradata : list with information on trained model, coming from mixed.solve

GROAN documentation built on Nov. 28, 2022, 5:07 p.m.