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Efficient simulation of genotype / phenotype data under assortative mating by generating Bahadur order-2 multivariate Bernoulli distributed random variates.
rb_dplr
: generate Bahadur order-2 MVB variates with
diagonal-plus-low-rank (DPLR) correlation structuresrb_unstr
: generate Bahadur order-2 MVB variates with
arbitrary correlation structuresh2_eq
: compute equilibrium heritabilityrg_eq
: compute equilibrium cross-mate genetic
correlationvg_eq
: compute equilibrium genetic varianceam_simulate
: complete univariate genotype / phenotype
simulationam_covariance_structure
: compute outer-product
covariance component for AM-induced DPLR covariance structurerBahadur
is now on CRAN:
install.packages("rBahadur")
Alternatively, you can install directly from github using the
install_github
function provided by the remotes
library:
::install_github("rborder/rBahadur") remotes
Here we demonstrate using rBahadur
to simulate genotype
/ phenotype at equilibrium under AM: given the following parameters:
h2_0
: panmictic heritabilityr
: cross-mate phenotypic correlationm
: number of diploid, biallelic causal variantsn
: number of individuals to simulatemin_MAF
: minimum minor allele frequencyset.seed(2022)
= .5; m = 2000; n = 5000; r =.5; min_MAF=.05
h2_0
## simulate genotype/phenotype data
<- am_simulate(h2_0, r, m, n) sim_dat
We compare the target and realized allele frequencies:
## plot empirical first moments of genotypes versus expectations
<- colMeans(sim_dat$X)/2
afs_emp plot(sim_dat$AF, afs_emp)
We compare the expected equilibrium heritability to that realized in simulation:
## empirical h2 vs expected equilibrium h2
<- var(sim_dat$g)/var(sim_dat$y))
(emp_h2 h2_eq(r, .5)
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
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.