load_input_and_run_cape: Loads input and run CAPE

In cape: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

Loads input and run CAPE

Description

This function loads the input file path and runs cape It is used to run CAPE from a non R script (python)

Usage

load_input_and_run_cape(
  input_file = NULL,
  yaml_params = NULL,
  results_path = NULL,
  run_parallel = FALSE,
  results_file = "cross.RDS",
  p_or_q = 0.05,
  n_cores = 4,
  initialize_only = FALSE,
  verbose = TRUE,
  param_file = NULL,
  create_report = FALSE,
  qtl_id_col = NULL,
  qtl_na_strings = "-"
)

Arguments

input_file	data input to be loaded
yaml_params	a parameter set up in the form of a YAML string
results_path	path to the results
run_parallel	boolean, if TRUE runs certain parts of the code as parallel blocks
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
n_cores	integer, default is 4
initialize_only	boolean, default: FALSE
verbose	boolean, output goes to stdout
param_file	path to yml parameter file for running cape
create_report	boolean, if true we create the corresponding HTML report page
qtl_id_col	argument for read_population, an optional column number for individual IDs
qtl_na_strings	argument for read_population, an optional string for missing values

cape documentation built on May 29, 2024, 5:11 a.m.