Package: AllelicSeries 0.0.4.1
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. (2022) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1101/2022.12.23.521658>.
Authors:
AllelicSeries_0.0.4.1.tar.gz
AllelicSeries_0.0.4.1.zip(r-4.5)AllelicSeries_0.0.4.1.zip(r-4.4)AllelicSeries_0.0.4.1.zip(r-4.3)
AllelicSeries_0.0.4.1.tgz(r-4.4-x86_64)AllelicSeries_0.0.4.1.tgz(r-4.4-arm64)AllelicSeries_0.0.4.1.tgz(r-4.3-x86_64)AllelicSeries_0.0.4.1.tgz(r-4.3-arm64)
AllelicSeries_0.0.4.1.tar.gz(r-4.5-noble)AllelicSeries_0.0.4.1.tar.gz(r-4.4-noble)
AllelicSeries_0.0.4.1.tgz(r-4.4-emscripten)AllelicSeries_0.0.4.1.tgz(r-4.3-emscripten)
AllelicSeries.pdf |AllelicSeries.html✨
AllelicSeries/json (API)
# Install 'AllelicSeries' in R: |
install.packages('AllelicSeries', repos = c('https://zmccaw-insitro.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 12 months agofrom:ffede88564. Checks:OK: 4 NOTE: 5. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 22 2024 |
R-4.5-win-x86_64 | NOTE | Aug 22 2024 |
R-4.5-linux-x86_64 | NOTE | Aug 22 2024 |
R-4.4-win-x86_64 | NOTE | Aug 22 2024 |
R-4.4-mac-x86_64 | NOTE | Aug 22 2024 |
R-4.4-mac-aarch64 | NOTE | Aug 22 2024 |
R-4.3-win-x86_64 | OK | Aug 22 2024 |
R-4.3-mac-x86_64 | OK | Aug 22 2024 |
R-4.3-mac-aarch64 | OK | Aug 22 2024 |
Exports:AggregatorASBTASKATCOASTComparatorDGPOLS
Dependencies:latticeMatrixplyrRcppRcppArmadilloRcppEigenRNOmniRSpectraSKATSPAtest
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Aggregator | Aggregator |
Allelic Series Burden Test | ASBT |
Allelic Series SKAT Test | ASKAT |
Calculate Regression Parameters | CalcRegParam |
Check Inputs | CheckInputs |
COding-variant Allelic Series Test | COAST |
Comparator Test | Comparator |
Data Generating Process | DGP |
Filter Noncausal Variants | FilterGenos |
Generate Genotype Annotations | GenAnno |
Generate Covariates | GenCovar |
Generate Genotypes | GenGeno |
Generate Genotype Matrix | GenGenoMat |
Generate Phenotypes | GenPheno |
Ordinary Least Squares | OLS |
Calculate Residual Variance | ResidVar |
Calculate Score Statistic | Score |