R/check_trait.R

In richelbilderbeek/plinkr: Interface to PLINK

#' Check if a trait is valid.
#'
#' Check if a trait (with a clear genetic architecture and a known
#' minor allele frequency) is valid.
#' Will \link{stop} if not
#'
#' @inheritParams default_params_doc
#' @return the checked trait, now of class type `trait`
#' @examples
#' check_trait(create_additive_trait())
#' check_trait(create_random_trait())
#' @export
#' @author Richèl J.C. Bilderbeek
check_trait <- function(trait) {
  testthat::expect_true(is.list(trait))
  testthat::expect_true("phenotype" %in% names(trait))
  testthat::expect_true("mafs" %in% names(trait))
  testthat::expect_true("n_snps" %in% names(trait))
  testthat::expect_true("calc_phenotype_function" %in% names(trait))
  plinkr::check_phenotypes(trait$phenotype)
  plinkr::check_mafs(trait$mafs)
  plinkr::check_n_snps(trait$n_snps)
  plinkr::check_calc_phenotype_function(
    calc_phenotype_function = trait$calc_phenotype_function
  )
  trait
}