The problem | How it works | A worked example | The assortative mating structure is preserved exactly | Local LD is preserved too | Choosing the number of causal variants | Working at realistic scale | Limitations
This package is considered a duplicate. The official version of this package is found at:https://border-lab.r-universe.dev/rBahadur
Package: rBahadur 1.1.0
Richard Border
rBahadur: Assortative Mating Simulation and Multivariate Bernoulli Variates
Simulation of phenotype / genotype data under assortative and disassortative mating. Includes functions for generating Bahadur order-2 multivariate Bernoulli variables with general and diagonal-plus-low-rank correlation structures, and for writing simulated genotypes to disk as binary int8 or PLINK bed files. Further details are provided in: Border and Malik (2023) <doi:10.1186/s12859-023-05442-6>.
Authors:
rBahadur_1.1.0.tar.gz
rBahadur_1.1.0.zip(r-4.7-any)
rBahadur_1.1.0.tar.gz(r-4.7-any)rBahadur_1.1.0.tar.gz(r-4.6-any)
rBahadur_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rBahadur/json (API)
| # Install 'rBahadur' in R: |
| install.packages('rBahadur', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/border-lab/rbahadur/issues
Last updated from:35a59a24b9. Checks:5 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 112 | ||
| source / vignettes | OK | 212 | ||
| linux-release-x86_64 | OK | 122 | ||
| windows-devel-x86_64 | OK | 87 | ||
| wasm-release | OK | 93 |
Exports:am_covariance_structuream_mosaicam_simulatedownload_1kg_panelh2_eqkg_referencerb_dplrrb_unstrrbahadur_cli_pathrbahadur_mainread_genotypesrg_eqvcf_to_panelvg_eqwrite_genotypes
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute Diagonal plus Low Rank equilibrium covariance structure | am_covariance_structure |
| Functions to compute equilibrium parameters under assortative mating | am_equilibrium_parameters h2_eq rg_eq vg_eq |
| Simulate equilibrium assortative mating with realistic local LD | am_mosaic |
| Simulate genotype/phenotype data under equilibrium univariate AM. | am_simulate |
| Download a 1000 Genomes region and build a reference panel | download_1kg_panel |
| Load the bundled 1000 Genomes reference panel | kg_reference |
| Binary random variates with Diagonal Plus Low Rank (dplr) correlations | rb_dplr |
| Binary random variates with unstructured correlations | rb_unstr |
| Path to the 'rbahadur' command line script | rbahadur_cli_path |
| Run the 'rbahadur' command line interface | rbahadur_main |
| Read genotypes from a binary file written by 'write_genotypes()' | read_genotypes |
| Build a reference panel from a VCF | vcf_to_panel |
| Write genotypes to a binary file | write_genotypes |
