blup: BLUP

In jendelman/StageWise: Two-stage analysis of multi-environment trials for genomic selection and GWAS

BLUP

Description

BLUP

Usage

blup(data, geno = NULL, what, index.coeff = NULL, gwas.ncore = 0L)

Arguments

data	one object, or list of objects, of class_prep from blup_prep
geno	object of class_geno from read_geno
what	One of the following: AV, BV, GV, AM, DM. See Details.
index.coeff	named vector of index coefficients for the locations or traits
gwas.ncore	Integer indicating number of cores to use for GWAS (default is 0 for no GWAS).

Details

The argument what takes 5 possible values: "AV" (additive value), "BV" (breeding value), "GV" (genotypic value), "AM" (additive marker effect), and "DM" (dominance marker effect). "Values" refer to predictions for individuals, as opposed to markers. Predicted values include the average fixed effect of the environments, whereas predicted marker effects do not. Argument index.coeff is a named vector (matching the names of the locations or traits), and the values are interpreted for standardized traits.

When multiple objects of class_prep are used for data, they must be based on the same marker data and genetic model. Also, reliabilities are not computed.

Value

Data frame of BLUPs

jendelman/StageWise documentation built on Feb. 23, 2025, 11 a.m.