AllelicSeries: Allelic Series Test

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>.

Version:	0.1.1.2
Imports:	CompQuadForm, glue, methods, Rcpp, RNOmni, SKAT
LinkingTo:	Rcpp, RcppArmadillo
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0), withr
Published:	2024-11-23
DOI:	10.32614/CRAN.package.AllelicSeries
Author:	Zachary McCaw [aut, cre], Christoph Klein [ctb], Thomas Soare [ctb], Jianhui Gao [ctb], insitro [cph]
Maintainer:	Zachary McCaw <zmccaw at insitro.com>
License:	BSD_3_clause + file LICENSE
URL:	https://github.com/insitro/AllelicSeries
NeedsCompilation:	yes
Materials:	NEWS
CRAN checks:	AllelicSeries results

Documentation:

Reference manual:	AllelicSeries.pdf
Vignettes:	COAST (source, R code) COAST-SS (source, R code) Data Generation (source, R code)

Downloads:

Package source:	AllelicSeries_0.1.1.2.tar.gz
Windows binaries:	r-devel: AllelicSeries_0.1.1.1.zip, r-release: AllelicSeries_0.1.0.2.zip, r-oldrel: AllelicSeries_0.1.0.2.zip
macOS binaries:	r-release (arm64): AllelicSeries_0.1.1.2.tgz, r-oldrel (arm64): AllelicSeries_0.1.1.2.tgz, r-release (x86_64): AllelicSeries_0.1.1.2.tgz, r-oldrel (x86_64): AllelicSeries_0.1.1.2.tgz
Old sources:	AllelicSeries archive

Linking:

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