run_cape {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.RDS",
  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,
  plot_pdf = TRUE
)

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 RDS file. The base name is used as the base name for all saved RDS 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.

plot_pdf

boolean, TRUE by default. If FALSE no pdf will be generated by the analysis.

Details

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

Value

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

Examples

## Not run: 
final_data_obj <- run_cape(pheno_obj, geno_obj)

## End(Not run)