simgenphen-package: Simulate Genotypes and Phenotypes

In OchoaLab/simgenphen: Simulate Genotypes and Phenotypes

Simulate Genotypes and Phenotypes

Description

The simgenphen package is a wrapper around several more specialized packages: bnpsd for admixture, simfam for family structure, and simtrait for complex traits. This package assumes reasonable defaults and generally saves on typing for some recurrent cases. Key non-trivial functionality is drawing genotypes for admixed families whose loci are all polymorphic.

Author(s)

Maintainer: Alejandro Ochoa [e-mail] (ORCID)

Examples

### one liner version
# admixture + family genotypes and phenotype
# run with default values, except smaller
data <- sim_gen_phen( n_ind = 50, G = 3, m_loci = 100, m_causal = 5 )

# main objects of interest:
# genotype matrix
data$X
# trait vector
data$trait

### version with separate steps
# More efficient in certain loops where population structure is constant
# but want newly-drawn genotypes and phenotypes.
# Also returns additional parameters

# first construct population parameters
# (relatedness but no loci)
k_subpops <- 3
data_pop <- sim_pop( n_ind = 50, G = 3, k_subpops = k_subpops )

# now draw genotypes!
m_loci <- 100
data_geno <- sim_geno(
    data_pop$admix_proportions_1,
    data_pop$inbr_subpops,
    data_pop$fam,
    data_pop$ids,
    m_loci
)

# genotype matrix
data_geno$X

# now draw trait!
m_causal <- 5
herit <- 0.5
data_trait <- sim_trait_env(
    data_geno$X,
    data_geno$p_anc,
    m_causal,
    herit,
    env = 'gcat',
    k_subpops = k_subpops
)

# the simulated trait
data_trait$trait
# indexes of randomly-selected causal loci
data_trait$causal_indexes
# coefficients of causal loci
data_trait$causal_coeffs

OchoaLab/simgenphen documentation built on Feb. 10, 2023, 3:32 p.m.