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: | 0.1.1.1 |
| Imports: | CompQuadForm, glue, methods, Rcpp, RNOmni, SKAT |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0), withr |
| Published: | 2024-11-22 |
| 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 [issues need fixing before 2024-12-06] |
Documentation:
| Reference manual: | AllelicSeries.pdf |
| Vignettes: |
COAST (source, R code) COAST-SS (source, R code) Data Generation (source, R code) |
Downloads:
| Package source: | AllelicSeries_0.1.1.1.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_0.1.0.2.tgz, r-oldrel (arm64): AllelicSeries_0.1.0.2.tgz, r-release (x86_64): AllelicSeries_0.1.1.1.tgz, r-oldrel (x86_64): AllelicSeries_0.1.1.1.tgz |
| Old sources: | AllelicSeries archive |
Linking:
Please use the canonical form https://CRAN.R-project.org/package=AllelicSeries to link to this page.