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CRAN DOI

Efficient simulation of genotype / phenotype data under assortative mating by generating Bahadur order-2 multivariate Bernoulli distributed random variates.

Features

Installation

rBahadur is now on CRAN:

install.packages("rBahadur")

Alternatively, you can install directly from github using the install_github function provided by the remotes library:

remotes::install_github("rborder/rBahadur")

Usage

Here we demonstrate using rBahadur to simulate genotype / phenotype at equilibrium under AM: given the following parameters:

set.seed(2022)
h2_0 = .5; m = 2000; n = 5000; r =.5; min_MAF=.05

## simulate genotype/phenotype data
sim_dat <- am_simulate(h2_0, r, m, n)

We compare the target and realized allele frequencies:


## plot empirical first moments of genotypes versus expectations
afs_emp <- colMeans(sim_dat$X)/2
plot(sim_dat$AF, afs_emp)

We compare the expected equilibrium heritability to that realized in simulation:


## empirical h2 vs expected equilibrium h2
(emp_h2 <- var(sim_dat$g)/var(sim_dat$y))
h2_eq(r, .5)

Citation

Developed by Richard Border and Osman Malik. For further details, or if you find this software useful, please cite: - Border, R. and Malik, O.A., 2022. rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating. BMC Bioinformatics. https://doi.org/10.1186/s12859-023-05442-6

Background reading:

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.