RAREsim

DOI: 10.18129/B9.bioc.RAREsim    

Simulation of Rare Variant Genetic Data

Bioconductor version: Release (3.16)

Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins - either as provided by default parameters or estimated from target data - and an abundance of rare variants as simulated HAPGEN2 to probabilistically prune variants. RAREsim produces haplotypes that emulate real sequencing data with respect to the total number of variants, allele frequency spectrum, haplotype structure, and variant annotation.

Author: Megan Null [aut], Ryan Barnard [cre]

Maintainer: Ryan Barnard <rbarnard1107 at gmail.com>

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

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("RAREsim")

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("RAREsim")

 

HTML R Script RAREsim Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Genetics, Sequencing, Software, VariantAnnotation
Version 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (0.5 years)
License GPL-3
Depends R (>= 4.1.0)
Imports nloptr
LinkingTo
Suggests markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL https://github.com/meganmichelle/RAREsim
BugReports https://github.com/meganmichelle/RAREsim/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package RAREsim_1.2.0.tar.gz
Windows Binary RAREsim_1.2.0.zip
macOS Binary (x86_64) RAREsim_1.2.0.tgz
macOS Binary (arm64) RAREsim_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RAREsim
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RAREsim
Package Short Url https://bioconductor.org/packages/RAREsim/
Package Downloads Report Download Stats

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