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simtrait
View on CRAN: Click
here
Download and install simtrait package within the R console
Install from CRAN:
install.packages("simtrait")
Install from Github:
library("remotes")
install_github("cran/simtrait")
Install by package version:
library("remotes")
install_version("simtrait", "1.1.3")
Attach the package and use:
library("simtrait")
Maintained by
Alejandro Ochoa
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-08-16
Latest Update: 2023-01-06
Description:
Simulate complex traits given a SNP genotype matrix and model parameters (the desired heritability, 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 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 (2022) <doi:10.1101/2022.03.25.485885>.
How to cite:
Alejandro Ochoa (2021). simtrait: Simulate Complex Traits from Genotypes. R package version 1.1.3, https://cran.r-project.org/web/packages/simtrait
Other packages that cited simtrait R package
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Other R packages that simtrait depends,
imports, suggests or enhances
Functions, R codes and Examples using
the simtrait R package
Some associated functions: allele_freqs . cov_trait . herit_loci . pval_aucpr . pval_infl . pval_power_calib . pval_srmsd . pval_type_1_err . rmsd . sim_trait . sim_trait_mvn . simtrait .
Some associated R codes: allele_freqs.R . check_herit_labs.R . cov_trait.R . herit_loci.R . pval_aucpr.R . pval_infl.R . pval_power_calib.R . pval_srmsd.R . pval_type_1_err.R . rmsd.R . select_loci.R . sim_trait.R . sim_trait_mvn.R . simtrait.R . sqrt_matrix.R . Full simtrait package functions and examples
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