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GVoverall

Source: vignettes/articles/criterion-gvoverall.Rmd
criterion-gvoverall.Rmd

GVoverall measures the total genetic variation covered by the training set: the generalized variance of its relationship matrix.

Type Genomic variation
Direction Larger is better
Uses a test set no (a test set given to optTrain() is ignored)
Score a given set gv_overall_score()
Search with it optTrain(method = "GVoverall")

Definition

With G=XX′/pG = XX'/p: log⁡det⁡G\log\det G (the log of the determinant in the benchmark of Fernández-González et al., 2023). It needs p≥np \ge n; use all PCs or markers.

Use in TSDFGS 

library(TSDFGS)
data(geno)
gv_overall_score(geno[1:50, ])
## [1] 169.8436
fit <- optTrain(geno, cand = 1:404, n.train = 50, method = "GVoverall",
                 min.iter = 300, console = FALSE, seed = 1)
fit$OPTtrain
##  [1] 324 244 314 299 402 315 321 253 216 185 398  49 103 328 262 278 296  20 392
## [20] 388 297 168 196  27 282 260 325 399 369 227 131 128 197 245  10 312  77 389
## [39] 256  16 135 268 149  60 152  62 350 316 298 138

The search is a random-start exchange (hill-climbing) search; see How the scores are computed. Use min.iter larger than 300 on real data and check fit$converged.

Original work

Fernández-González, J., Akdemir, D., & Isidro y Sánchez, J. (2023). A comparison of methods for training population optimization in genomic selection. Theoretical and Applied Genetics, 136, 30. https://doi.org/10.1007/s00122-023-04265-6

Chen, S.-P., Sung, W.-H., & Liao, C.-T. (2024). Constructing training sets for genomic selection to identify superior genotypes in candidate populations. Theoretical and Applied Genetics, 137, 270. https://doi.org/10.1007/s00122-024-04766-y

Repository or website of the original authors: Code of Fernández-González et al. (2023): github.com/TheRocinante-lab/Publications. Package TrainSel: github.com/TheRocinante-lab/TrainSel. R package TSODBG of Chen et al. (2024): github.com/spcspin/TSODBG (GPL >= 3).

License review

Formulas and algorithms are ideas and methods, which copyright does not protect. Where an original package is under a GPL license, we read it to check our results and credit it; TSDFGS is GPL-3, which is compatible with GPL-3 and GPL (>= 3) code. This is our reading of the public record, not legal advice; see the license review.

  • Original software: the repository of Fernández-González et al. (2023) has no LICENSE file, and TrainSel carries an all-rights-reserved license with a patent notice. We did not read or copy either; the definition comes from the open-access article.
  • TSODBG: GPL (>= 3); compared, not copied.
  • Article license: Fernández-González et al. (2023) CC BY 4.0.
  • Verdict: included, written from the article.

Reviewed 2026-11-04. All criteria and the ones left out.