Package: BreedingExperiment
Title: Container and Relationship Matrices for Breeding and
        Quantitative Genomics
Version: 0.99.4
Authors@R: 
    person("Muhammad", "Farooqi", email = "mqfarooqi@gmail.com",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-4918-9791"))
Description: Provides the BreedingExperiment class, a container that
        keeps marker genotypes, phenotypes, pedigree and marker
        coordinates together in one object, extending
        RangedSummarizedExperiment so that markers are addressable as
        genomic ranges. Relationship matrices central to quantitative
        genetics are computed as methods on the container: the pedigree
        numerator relationship matrix of Henderson (1976)
        <doi:10.2307/2529339>, the genomic relationship matrix of
        VanRaden (2008) <doi:10.3168/jds.2007-0980>, the dominance
        relationship matrix of Vitezica, Varona and Legarra (2013)
        <doi:10.1534/genetics.113.155176>, and the single-step matrix
        combining pedigree and genomic information of Legarra, Aguilar
        and Misztal (2009) <doi:10.3168/jds.2009-2061> and Christensen
        and Lund (2010) <doi:10.1186/1297-9686-42-2>, which allows
        genotyped and ungenotyped individuals to be analysed together
        as in Aguilar and others (2010) <doi:10.3168/jds.2009-2730>.
        Marker quality control, imputation, inbreeding coefficients and
        allele frequency summaries are included.
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-GB
Depends: R (>= 4.5.0), SummarizedExperiment
Imports: methods, stats, utils, S4Vectors, GenomicRanges, IRanges,
        BiocGenerics
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
biocViews: Software, Genetics, SNP, GenomicVariation,
        DataRepresentation, Infrastructure, Regression, QualityControl
URL: https://github.com/mqfarooqi1/BreedingExperiment,
        https://mqfarooqi1.github.io/BreedingExperiment/
BugReports: https://github.com/mqfarooqi1/BreedingExperiment/issues
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
Collate: 'AllClasses.R' 'AllGenerics.R' 'BreedingExperiment-package.R'
        'constructor.R' 'accessors.R' 'pedigree.R' 'relationship.R'
        'singlestep.R' 'qc.R' 'simulate.R' 'data.R' 'show.R'
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-07-31 00:03:03 UTC
RemoteUrl: https://github.com/BiocStaging/BreedingExperiment
RemoteRef: HEAD
RemoteSha: 278f08e281e6b9c5da67ed59a13d0ec0c3cafdd7
NeedsCompilation: no
Packaged: 2026-09-29 07:19:45 UTC; root
Author: Muhammad Farooqi [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4918-9791>)
Maintainer: Muhammad Farooqi <mqfarooqi@gmail.com>