Package: AllelicSeries
Title: Allelic Series Test
Version: 0.1.1.5
Authors@R: 
    c(person(given = "Zachary",
           family = "McCaw",
           email = "zmccaw@alumni.harvard.edu",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-2006-9828")),
	person(given = "Christoph",
           family = "Klein",
           email = "cklein@insitro.com",
           role = "ctb",
           comment = c(ORCID = "0000-0002-1748-625X")),
	person(given = "Thomas",
           family = "Soare",
           email = "tsoare@insitro.com",
           role = "ctb",
           comment = c(ORCID = "0000-0002-4903-8646")),
	person(given = "Jianhui",
	   family = "Gao",
	   email = "jianhui.gao@mail.utoronto.ca",
	   role = "ctb",
	   comment = c(ORCID = "0000-0003-0915-1473")),
	person(given = "insitro", role = c("cph"))
    )
Description: Implementation of gene-level rare variant association
        tests targeting allelic series: genes where increasingly
        deleterious mutations have increasingly large phenotypic
        effects. The COding-variant Allelic Series Test (COAST)
        operates on the benign missense variants (BMVs), deleterious
        missense variants (DMVs), and protein truncating variants
        (PTVs) within a gene. COAST uses a set of adjustable weights
        that tailor the test towards rejecting the null hypothesis for
        genes where the average magnitude of effect increases
        monotonically from BMVs to DMVs to PTVs. See McCaw ZR,
        O’Dushlaine C, Somineni H, Bereket M, Klein C, Karaletsos T,
        Casale FP, Koller D, Soare TW. (2023) "An allelic series rare
        variant association test for candidate gene discovery"
        <doi:10.1016/j.ajhg.2023.07.001>.
License: BSD_3_clause + file LICENSE
URL: https://github.com/insitro/AllelicSeries
Encoding: UTF-8
Imports: CompQuadForm, glue, methods, Rcpp, RNOmni, SKAT
LinkingTo: Rcpp, RcppArmadillo
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), withr
Config/testthat/edition: 3
VignetteBuilder: knitr
Repository: https://insitro.r-universe.dev
Date/Publication: 2025-10-22 19:31:46 UTC
RemoteUrl: https://github.com/insitro/allelicseries
RemoteRef: HEAD
RemoteSha: f7c182fc2ef25d78476ab97022db1160c7631e8c
NeedsCompilation: yes
Packaged: 2026-06-19 07:54:30 UTC; root
Author: Zachary McCaw [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2006-9828>),
  Christoph Klein [ctb] (ORCID: <https://orcid.org/0000-0002-1748-625X>),
  Thomas Soare [ctb] (ORCID: <https://orcid.org/0000-0002-4903-8646>),
  Jianhui Gao [ctb] (ORCID: <https://orcid.org/0000-0003-0915-1473>),
  insitro [cph]
Maintainer: Zachary McCaw <zmccaw@alumni.harvard.edu>