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) as implemented in 'GMMAT', and the per-ancestry p-values are combined with the Cauchy combination test of Liu and Xie (2020) . 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 Config/pak/sysreqs: cmake make libicu-dev libx11-dev zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-10-29 18:25:33 UTC RemoteUrl: https://github.com/bioc/lantern RemoteRef: HEAD RemoteSha: aec0b2441cf3c2da8c3f02f6210ccfc9e24f3b9b NeedsCompilation: yes Packaged: 2026-11-04 14:47:33 UTC; root Author: Yu Wang [aut, cre], Bjoernar Tuftin [aut], Paul Auer [aut] Maintainer: Yu Wang