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RVS

Computes estimates of the probability of related individuals sharing a rare variant


Bioconductor version: Release (3.18)

Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).

Author: Alexandre Bureau, Ingo Ruczinski, Samuel Younkin, Thomas Sherman

Maintainer: Thomas Sherman <tomsherman159 at gmail.com>

Citation (from within R, enter citation("RVS")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RVS")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RVS")
The RVS Package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ExomeSeq, Genetics, GenomeWideAssociation, ImmunoOncology, Software, VariantDetection, WholeGenome
Version 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-2
Depends R (>= 3.5.0)
Imports GENLIB, gRain, snpStats, kinship2, methods, stats, utils
System Requirements
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Suggests knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package RVS_1.24.0.tar.gz
Windows Binary RVS_1.24.0.zip
macOS Binary (x86_64) RVS_1.24.0.tgz
macOS Binary (arm64) RVS_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RVS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RVS
Bioc Package Browser https://code.bioconductor.org/browse/RVS/
Package Short Url https://bioconductor.org/packages/RVS/
Package Downloads Report Download Stats