cape (version 3.1.0)

run_cape: Runs CAPE

Description

This function takes in a data object and genotype object that have been formatted for cape, as well as a string identifying a parameter file. It runs cape on the data using the parameters specified in the file.

Usage

run_cape(
  pheno_obj,
  geno_obj,
  results_file = "cross.RData",
  p_or_q = 0.05,
  n_cores = 4,
  initialize_only = FALSE,
  verbose = TRUE,
  run_parallel = FALSE,
  param_file = NULL,
  yaml_params = NULL,
  results_path = NULL
)

Arguments

pheno_obj

the cape object holding the phenotype data returned by

geno_obj

the genotype object

results_file

the name of the saved data_obj RData file. The base name is used as the base name for all saved RData files.

p_or_q

A threshold indicating the maximum adjusted p value considered significant. Or, if FDR p value correction is used, the the maximum q value considered significant.

n_cores

The number of CPUs to use if run_parallel is set to TRUE

initialize_only,

If TRUE, cape will not be run. Instead an initialized data object will be returned. This data object will contain normalized and mean-centered trait values, and eigentraits, and will have covariates specified. However, the singlescan, pairscan, etc. will not be run.

verbose

Whether progress should be printed to the screen

run_parallel

boolean, if TRUE runs certain parts of the code as parallel blocks

param_file

yaml full path to the parameter file

yaml_params

yaml string containing the parameters. Either the param_file or yaml_params can be null.

results_path

path that results should be written to.

Value

This function invisibly returns the data object with all final data included. In addition, data saved to the data_obj$results_path directory

Details

This function assumes you already have all required libraries and functions loaded.

Examples

# NOT RUN {
final_data_obj <- run_cape(pheno_obj, geno_obj)
# }
# NOT RUN {
# }