gain: Genetic gain

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

Genetic gain

Description

Genetic gain calculations

Usage

gain(
  input,
  merit = NULL,
  desired = NULL,
  restricted = NULL,
  traits = NULL,
  gamma = NULL,
  solver = "ECOS",
  ...
)

Arguments

input	either object of class_prep or quad.mat returned by this function
merit	named vector of merit coefficients, in genetic standard deviation units
desired	named vector of desired gains, in genetic standard deviation units
restricted	data frame of restricted traits, see Details
traits	optional vector with exactly 2 trait names, to plot elliptical response
gamma	contribution of non-additive values for genetic merit
solver	name of convex solver (default is "ECOS")

Details

Either merit or desired can be used, not both. The former specifies the relative contribution of each trait to genetic merit, while the latter specifies the relative desired gain in genetic standard deviation units. All traits must be specified. Optional argument restricted is a data frame with columns "trait" and "sign", where the options for sign are "=",">","<", representing equal to zero, non-negative, and non-positive. When desired is used, the restricted argument is ignored.

The argument gamma controls the definition of genetic merit. (See notation in the journal publication.) The default is NULL, which implies breeding values. For purely additive values, use gamma = 0. For total genotypic value, use gamma = 1.

Note that this function assumes a selection index of BLUPs, not phenotypes.

Value

List containing

quad.mat

quadratic matrix for the ellipsoid

plot

ellipse plot

table

data frame with the response and index coefficients for all traits

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