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>.

Package overview COAST from Summary Statistics Coding-variant Allelic Series Test Covariate Inference Data Generation

Vignettes Man pages API and functions Files

Package details
Author	Zachary McCaw [aut, cre] (<https://orcid.org/0000-0002-2006-9828>), Christoph Klein [ctb] (<https://orcid.org/0000-0002-1748-625X>), Thomas Soare [ctb] (<https://orcid.org/0000-0002-4903-8646>), Jianhui Gao [ctb] (<https://orcid.org/0000-0003-0915-1473>), insitro [cph]
Maintainer	Zachary McCaw <zmccaw@alumni.harvard.edu>
License	BSD_3_clause + file LICENSE
Version	0.1.1.5
URL	https://github.com/insitro/AllelicSeries
Package repository	View on CRAN
Installation	Install the latest version of this package by entering the following in R: `install.packages("AllelicSeries")`