Changelog

Source: NEWS.md

BreedingExperiment 0.99.4

• Documented the return value on the class page, clearing the BiocCheck warning about a missing alue section.
• Wrapped the last over-long source line.

BreedingExperiment 0.99.3

• Version bump only, to re-run the Bioconductor checks after a transient bioconductor.org outage (HTTP 504) aborted BiocCheck. No code changes.

BreedingExperiment 0.99.2

• Split simulateBreeding() into helpers so no function exceeds the recommended length.
• Wrapped over-long source lines and added the QualityControl biocView.

BreedingExperiment 0.99.1

• Removed a non-standard field from DESCRIPTION.
• Added citation metadata (inst/CITATION and CITATION.cff).

BreedingExperiment 0.99.0

First submission to Bioconductor.

• The BreedingExperiment class, extending RangedSummarizedExperiment, holds marker genotypes, phenotypes, a pedigree and marker coordinates in one object.
• Relationship matrices: Amatrix() (pedigree), Gmatrix() (genomic), Dmatrix() (dominance) and Hmatrix() (single step, combining pedigree and genomic information so genotyped and ungenotyped individuals can be analysed together).
• Quality control with filterMarkers() and imputeMarkers(), plus alleleFrequency(), inbreeding() and sortPedigree().
• demoBreeding, a simulated five-generation population with ungenotyped ancestors, and simulateBreeding() for generating your own.