Overview of RAREsim | Step (1): Simulate an abundance of rare variants | Step (2): Estimate the expected number of rare variants | Step (3): Probabilistically prune the rare variants | Installing the RAREsim Package | RAREsim R package: Estimate expected number of rare variants per MAC bin | The Number of Variants function | 1) Fitting Target Data | 2) Using Default Parameters | 3) Directly Inputting Parameters | Total Number of Variants in the Region | The Allele Frequency Spectrum (AFS) Function | Combining Funcitons to Get Expected Variants | Session Info
Package: RAREsim 1.17.0
Ryan Barnard
RAREsim: Simulation of Rare Variant Genetic Data
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.
Authors:
RAREsim_1.17.0.tar.gz
RAREsim_1.17.0.zip(r-4.7)RAREsim_1.17.0.zip(r-4.6)RAREsim_1.17.0.zip(r-4.5)
RAREsim_1.17.0.tgz(r-4.6-any)RAREsim_1.17.0.tgz(r-4.5-any)
RAREsim_1.17.0.tar.gz(r-4.7-any)RAREsim_1.17.0.tar.gz(r-4.6-any)
RAREsim_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RAREsim/json (API)
| # Install 'RAREsim' in R: |
| install.packages('RAREsim', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/meganmichelle/raresim/issues
Datasets:
- afs_afr - African/African American target data from gnomAD v2.1
- nvariant_afr - African target data for the Number of Variants function from gnomADv2.1
On BioConductor:RAREsim-1.17.0(bioc 3.24)RAREsim-1.16.0(bioc 3.23)
geneticssoftwarevariantannotationsequencing
Last updated from:8150389173. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 141 | ||
| linux-devel-x86_64 | OK | 146 | ||
| source / vignettes | OK | 215 | ||
| linux-release-x86_64 | OK | 172 | ||
| macos-release-arm64 | OK | 102 | ||
| macos-oldrel-arm64 | OK | 89 | ||
| windows-devel | OK | 77 | ||
| windows-release | OK | 84 | ||
| windows-oldrel | OK | 84 | ||
| wasm-release | OK | 105 |
Exports:afsexpected_variantsfit_afsfit_nvariantnvariant
Dependencies:nloptr
