set.seed(1234)
library(cape)
results_path <- here::here("demo", "demo_rds")
data_path <- here::here("tests", "testthat", "testdata", "demo_rds_data")
data_file <- file.path(data_path, "cape_data.RDS")
geno_file <- file.path(data_path, "cape_geno.RDS")
cape_obj <- readRDS(data_file)
cape_geno <- readRDS(geno_file)
param_file <- file.path(results_path, "NON_NZO.parameters.yml")
# genotype coding
het_val <- 0.3 #could be 0.5, but I think we can go as low as 0.3
dom_geno <- cape_geno
for(i in 1:dim(dom_geno)[3]){
dom_mat <- dom_geno[,,i]
dom_mat[which(dom_mat >= het_val)] <- 1
dom_mat[which(dom_mat < het_val)] <- 0
dom_geno[,,i] <- dom_mat
}
cross_obj <- Cape$new(
parameter_file = param_file,
results_path = results_path,
pheno = cape_obj$pheno,
chromosome = cape_obj$chromosome,
marker_num = cape_obj$marker_num,
marker_location = cape_obj$marker_location,
geno_names = cape_obj$geno_names,
geno = dom_geno
)
final_cross <- run_cape(pheno_obj = cross_obj, geno_obj = cape_geno, p_or_q = 0.05,
results_path = results_path, param_file = param_file)
plot_variant_influences(final_cross)
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