Package: GENESIS
Type: Package
Title: GENetic EStimation and Inference in Structured samples
        (GENESIS): Statistical methods for analyzing genetic data from
        samples with population structure and/or relatedness
Version: 2.42.0
Date: 2025-01-31
Authors@R: c(
  person(c("Matthew", "P."), "Conomos", role = c("aut")),
  person(c("Stephanie", "M."), "Gogarten", email = "sdmorris@uw.edu", role = c("aut", "cre")),
  person("Lisa", "Brown", role = "aut"),
  person("Han", "Chen", role = "aut"),
  person("Thomas", "Lumley", role = "aut"),
  person("Kenneth", "Rice", role = "aut"),
  person("Tamar", "Sofer", role = "aut"),
  person("Adrienne", "Stilp", role = "aut"),
  person("Timothy", "Thornton", role = "aut"),
  person("Chaoyu", "Yu", role = "aut"))
Description: The GENESIS package provides methodology for estimating,
        inferring, and accounting for population and pedigree structure
        in genetic analyses.  The current implementation provides
        functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate
        (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components
        Analysis on genome-wide SNP data for the detection of population
        structure in a sample that may contain known or cryptic relatedness.
        Unlike standard PCA, PC-AiR accounts for relatedness in the sample
        to provide accurate ancestry inference that is not confounded by
        family structure. PC-Relate uses ancestry representative principal
        components to adjust for population structure/ancestry and accurately
        estimate measures of recent genetic relatedness such as kinship
        coefficients, IBD sharing probabilities, and inbreeding coefficients.
        Additionally, functions are provided to perform efficient variance
        component estimation and mixed model association testing for both
        quantitative and binary phenotypes.
License: GPL-3
URL: https://github.com/UW-GAC/GENESIS
Depends:
Imports: Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt,
        GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools,
        SNPRelate, data.table, graphics, grDevices, igraph, Matrix,
        methods, reshape2, stats, utils
Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey,
        testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr,
        ggplot2, GGally, RColorBrewer,
        TxDb.Hsapiens.UCSC.hg19.knownGene, GenomeInfoDb
VignetteBuilder: knitr
biocViews: SNP, GeneticVariability, Genetics, StatisticalMethod,
        DimensionReduction, PrincipalComponent, GenomeWideAssociation,
        QualityControl, BiocViews
NeedsCompilation: yes
RoxygenNote: 7.3.3
git_url: https://git.bioconductor.org/packages/GENESIS
git_branch: RELEASE_3_23
git_last_commit: 2d7b4fe
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
Packaged: 2026-04-28 22:15:03 UTC; biocbuild
Author: Matthew P. Conomos [aut],
  Stephanie M. Gogarten [aut, cre],
  Lisa Brown [aut],
  Han Chen [aut],
  Thomas Lumley [aut],
  Kenneth Rice [aut],
  Tamar Sofer [aut],
  Adrienne Stilp [aut],
  Timothy Thornton [aut],
  Chaoyu Yu [aut]
Maintainer: Stephanie M. Gogarten <sdmorris@uw.edu>
Built: R 4.6.0; aarch64-apple-darwin23; 2026-04-29 04:44:16 UTC; unix
