Package: simtrait 1.1.9.9000
Alejandro Ochoa
simtrait: Simulate Complex Traits from Genotypes
Simulate complex traits given a SNP genotype matrix and model parameters (the desired heritability, optional environment group effects, number of causal loci, and either the true ancestral allele frequencies used to generate the genotypes or the mean kinship for a real dataset). Emphasis is on avoiding common biases due to the use of estimated allele frequencies. The code selects random loci to be causal, constructs coefficients for these loci and random independent non-genetic effects, and can optionally generate random group effects. Traits can follow three models: random coefficients, fixed effect sizes, and infinitesimal (multivariate normal). GWAS method benchmarking functions are also provided. Described in Yao and Ochoa (2023) <doi:10.7554/eLife.79238>.
Authors:
simtrait_1.1.9.9000.tar.gz
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simtrait.pdf |simtrait.html✨
simtrait/json (API)
NEWS
| # Install 'simtrait' in R: |
| install.packages('simtrait', repos = c('https://ochoalab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ochoalab/simtrait/issues
Last updated 3 months agofrom:dc8be4f16e. Checks:8 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 28 2025 |
| R-4.5-win | OK | Feb 28 2025 |
| R-4.5-mac | OK | Feb 28 2025 |
| R-4.5-linux | OK | Feb 28 2025 |
| R-4.4-win | OK | Feb 28 2025 |
| R-4.4-mac | OK | Feb 28 2025 |
| R-4.3-win | OK | Feb 28 2025 |
| R-4.3-mac | OK | Feb 28 2025 |
Exports:allele_freqscov_traitherit_lociinv_var_est_bayesianp_anc_est_beta_mlepval_aucprpval_gcpval_inflpval_power_calibpval_srmsdpval_type_1_errrmsdsim_traitsim_trait_mvn
Dependencies:PRROC
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute locus allele frequencies | allele_freqs |
| The model covariance matrix of the trait | cov_trait |
| Per-locus heritability contribution from allele frequency and causal coefficient | herit_loci |
| Calculate expectations of inverse variance terms over the posterior distribution of the ancestral allele frequency | inv_var_est_bayesian |
| Calculate maximum likelihood estimates of allele frequencies from Beta model | p_anc_est_beta_mle |
| Area under the precision-recall curve | pval_aucpr |
| Apply genomic control transformation to a list of p-values | pval_gc |
| Calculate inflation factor from p-values | pval_infl |
| Estimate calibrated power | pval_power_calib |
| Signed RMSD measure of null p-value uniformity | pval_srmsd |
| Estimate type I error rate | pval_type_1_err |
| Root mean square deviation | rmsd |
| Simulate a complex trait from genotypes | sim_trait |
| Simulate traits from a kinship matrix under the infinitesimal model | sim_trait_mvn |
| simtrait: simulate complex traits from genotypes | simtrait-package simtrait |
