Switch to Gmatrix

[alex-sandercock]

Updated the genomic selection tabs to use Gmatrix for the additive relationship matrices.

[Copilot]

Pull Request Overview

This PR updates the genomic selection modules to use AGHmatrix’s Gmatrix for computing additive relationship matrices instead of rrBLUP’s A.mat.

• Switched A.mat calls to Gmatrix with VanRaden method and additional parameters.
• Commented out the custom convert_genotype function and its usages in favor of raw genotype inputs.
• Adjusted get_relationship_mat and format_geno_matrix to integrate Gmatrix logic.

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
R/mod_GS.R	Switched from A.mat to Gmatrix, commented out unused genotype conversion logic, added AGHmatrix import
R/GS_functions.R	Replaced A.mat with Gmatrix in get_relationship_mat, refined condition in format_geno_matrix

Comments suppressed due to low confidence (4)

R/GS_functions.R:203

• After switching to Gmatrix, consider adding or updating unit tests to cover the new relationship matrix logic and parameter handling.

    Geno.mat <- Gmatrix(t(geno_input),

R/GS_functions.R:203

• The variable ploidy is referenced in the Gmatrix call but is not defined or passed into get_relationship_mat. Consider adding a ploidy parameter to the function signature or deriving it appropriately.

    Geno.mat <- Gmatrix(t(geno_input),

R/mod_GS.R:644

• [nitpick] The convert_genotype function and its usages are commented out and no longer needed. Removing this dead code will improve readability and maintainability.

    #convert_genotype <- function(genotype_matrix, ploidy) {

R/GS_functions.R:385

• [nitpick] In R, use && for scalar logical comparisons instead of & to avoid unintended vectorized operations.

  if(model == "rrBLUP" & ploidy == 2 & pred_matrix == "Gmatrix") {