#' Read the parameter file, add missing entries
#'
#' This function returns reads in the YAML file
#' and checks for any parameters that might not
#' be included. This may not matter for the given
#' run, but it's handy to be able to check for
#' any and all potential variables.
#'
#' @param filename full path to the .yml file holding CAPE parameters (is not needed if yaml_parameters is provided)
#' @param yaml_parameters yaml string holding CAPE parameters (can be NULL)
#'
#' @return Returns a named list with all possible options
#'
#' @import yaml
#'
#' @export
read_parameters <- function(filename = "cape.parameters.yml", yaml_parameters = NULL){
if (!is.null(yaml_parameters)) {
parameter_table <- yaml.load(yaml_parameters)
} else {
parameter_table <- read_yaml(filename)
}
#================================================
# general parameters
#================================================
gen_param <- c("traits", "covariates", "marker_covariates", "traits_scaled", "traits_normalized", "scan_what", "eig_which", "use_kinship", "kinship_type", "locus", "pop", "pval_correction", "transform_to_phenospace")
#================================================
#single scan parameters
#================================================
single_param <- c("ref_allele", "singlescan_perm", "alpha")
#================================================
# marker selection
#================================================
marker.param <- c("marker_selection_method", "snp_file", "peak_density", "tolerance", "window_size", "num_alleles_in_pairscan", "bp_buffer", "organism")
#================================================
# pair scan
#================================================
pair_param <- c("max_pair_cor", "min_per_genotype", "pairscan_null_size")
for ( param_name in c(gen_param, single_param, marker.param, pair_param) ) {
if ( !is.element(param_name, names(parameter_table)) ){
parameter_table[param_name] = NULL
}
}
return(parameter_table)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.