Package: lantern
Type: Package
Title: Ancestry-Specific Rare Variant Association Analysis
Version: 0.99.1
Authors@R: c(
    person(given = "Yu",
           family = "Wang",
           role = c("aut", "cre"),
           email = "ywang@mcw.edu"),
    person(given = "Bjoernar",
           family = "Tuftin",
           role = "aut",
           email = "btuftin@email.unc.edu"),
    person(given = "Paul",
           family = "Auer",
           role = "aut",
           email = "pauer@mcw.edu"))
Description: Ancestry-specific rare variant burden testing for admixed
    populations. Splits genotype dosages by local ancestry (as inferred by
    'RFMix') into per-ancestry dosages, using either phased haplotypes or
    unphased genotypes, where ambiguous mixed-ancestry heterozygotes are
    split with shrinkage toward 1/2, and writes
    them to 'SeqArray' GDS files. Ancestry-stratified gene-level tests are
    then run with the 'SMMAT' framework of Chen et al. (2019)
    <doi:10.1016/j.ajhg.2018.12.012> as implemented in 'GMMAT', and the
    per-ancestry p-values are combined with the Cauchy combination test of
    Liu and Xie (2020) <doi:10.1080/01621459.2018.1554485>.
URL: https://yuw444.github.io/lantern/,
        https://github.com/yuw444/lantern
BugReports: https://github.com/yuw444/lantern/issues
SystemRequirements: bcftools (>= 1.10) (optional; faster VCF reading
        and BCF input)
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: data.table, GMMAT, SeqArray, SeqVarTools, stats, utils
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: Software, Genetics, GenomeWideAssociation, SNP,
        VariantAnnotation
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
git_url: https://git.bioconductor.org/packages/lantern
git_branch: devel
git_last_commit: aec0b24
git_last_commit_date: 2026-10-29
Repository: Bioconductor 3.24
Date/Publication: 2026-11-04
NeedsCompilation: yes
Packaged: 2026-11-04 23:41:38 UTC; biocbuild
Author: Yu Wang [aut, cre],
  Bjoernar Tuftin [aut],
  Paul Auer [aut]
Maintainer: Yu Wang <ywang@mcw.edu>
