Package: AllelicSeries 0.1.1.5

Zachary McCaw

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>.

Authors:Zachary McCaw [aut, cre], Christoph Klein [ctb], Thomas Soare [ctb], Jianhui Gao [ctb], insitro [cph]

AllelicSeries_0.1.1.5.tar.gz
AllelicSeries_0.1.1.5.zip(r-4.7-x86_64)AllelicSeries_0.1.1.5.zip(r-4.7-arm64)AllelicSeries_0.1.1.5.zip(r-4.6-x86_64)AllelicSeries_0.1.1.5.zip(r-4.6-arm64)AllelicSeries_0.1.1.5.zip(r-4.5-x86_64)
AllelicSeries_0.1.1.5.tgz(r-4.6-x86_64)AllelicSeries_0.1.1.5.tgz(r-4.6-arm64)AllelicSeries_0.1.1.5.tgz(r-4.5-x86_64)AllelicSeries_0.1.1.5.tgz(r-4.5-arm64)
AllelicSeries_0.1.1.5.tar.gz(r-4.7-arm64)AllelicSeries_0.1.1.5.tar.gz(r-4.7-x86_64)AllelicSeries_0.1.1.5.tar.gz(r-4.6-arm64)AllelicSeries_0.1.1.5.tar.gz(r-4.6-x86_64)
AllelicSeries_0.1.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AllelicSeries/json (API)

# Install 'AllelicSeries' in R:
install.packages('AllelicSeries', repos = c('https://insitro.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/insitro/allelicseries/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

openblascppopenmp

6.13 score 14 stars 16 scripts 443 downloads 18 exports 12 dependencies

Last updated from:f7c182fc2e. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK153
linux-devel-x86_64OK176
source / vignettesOK206
linux-release-arm64OK151
linux-release-x86_64OK147
macos-release-arm64OK160
macos-release-x86_64OK361
macos-oldrel-arm64OK210
macos-oldrel-x86_64OK454
windows-devel-arm64OK394
windows-devel-x86_64OK331
windows-release-arm64OK397
windows-release-x86_64OK167
windows-oldrel-x86_64OK178
wasm-releaseOK132

Exports:AggregatorASBTASBTSSASKATASKATSSBaselineSSCalcSumstatsCOASTCOASTSSCollapseGenoComparatorContainsIntCountsDGPGenomicControlisPDOLSSumCountSS

Dependencies:CompQuadFormgluelatticeMatrixplyrRcppRcppArmadilloRcppEigenRNOmniRSpectraSKATSPAtest

Coding-variant Allelic Series Test
Data | Running the alleic series test | Ultra-rare variants | Different numbers of annotation categories | Test options
Rendered fromcoast.Rmdusingknitr::rmarkdown

Last update: 2025-04-02
Started: 2022-12-23

Covariate Inference
Overview | Example data | Score tests | Wald tests
Rendered fromcovariate_inference.Rmdusingknitr::rmarkdown

Last update: 2025-01-07
Started: 2025-01-07

COAST from Summary Statistics
Overview | Summary statistics | COAST-SS | Alternating weighting schemes | Different numbers of annotation categories | Test options
Rendered fromcoast_ss.Rmdusingknitr::rmarkdown

Last update: 2024-11-22
Started: 2024-11-14

Data Generation
Overview | Baseline model | Allelic sum model | Allelic max model | Allelic SKAT model | Simulating more than 3 annotation categories | Additional arguments
Rendered fromdata_generation.Rmdusingknitr::rmarkdown

Last update: 2024-11-14
Started: 2024-11-14