Package: AllelicSeries 0.1.1.2

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_0.1.1.2.tar.gz
AllelicSeries_0.1.1.2.tar.gz(r-4.5-noble)AllelicSeries_0.1.1.2.tar.gz(r-4.4-noble)
AllelicSeries_0.1.1.2.tgz(r-4.4-emscripten)AllelicSeries_0.1.1.2.tgz(r-4.3-emscripten)
AllelicSeries.pdf |AllelicSeries.html
AllelicSeries/json (API)
NEWS

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

Peer review:

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

2.78 score 7 scripts 728 downloads 16 exports 12 dependencies

Last updated 15 days agofrom:5f928beb03. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 24 2024
R-4.5-linux-x86_64OKNov 24 2024

Exports:AggregatorASBTASBTSSASKATASKATSSBaselineSSCalcSumstatsCOASTCOASTSSComparatorCountsDGPGenomicControlisPDOLSSumCountSS

Dependencies:CompQuadFormgluelatticeMatrixplyrRcppRcppArmadilloRcppEigenRNOmniRSpectraSKATSPAtest

Coding-variant Allelic Series Test

Rendered fromcoast.Rmdusingknitr::rmarkdownon Nov 24 2024.

Last update: 2024-11-22
Started: 2023-01-13

COAST from Summary Statistics

Rendered fromcoast_ss.Rmdusingknitr::rmarkdownon Nov 24 2024.

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

Data Generation

Rendered fromdata_generation.Rmdusingknitr::rmarkdownon Nov 24 2024.

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