set.seed(1234)
library(cape)
results_path <- here::here("demo", "demo_PLINK")
data_path <- here::here("tests", "testthat", "testdata", "demo_PLINK_data")
ped <- file.path(data_path, "test.ped")
map <- file.path(data_path, "test.map")
pheno <- file.path(data_path, "test.pheno")
out <- file.path(data_path, "test.csv")
param_file <- file.path(results_path, "plink.parameters.yml")
cross_obj <- plink2cape(ped, map, pheno, out, overwrite = TRUE)
data_obj <- cross_obj$data_obj
geno_obj <- cross_obj$geno_obj$geno
final_cross <- run_cape(pheno_obj = data_obj, geno_obj,
p_or_q = 0.05, verbose = TRUE, param_file = param_file,
results_path = results_path)
plot_variant_influences(final_cross)
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