load_input_and_run_cape {cape}R Documentation

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.RData",
  p_or_q = 0.05,
  n_cores = 4,
  initialize_only = FALSE,
  verbose = TRUE
)

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 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

n_cores

integer, default is 4

initialize_only

boolean, default: FALSE

verbose

boolean, output goes to stdout

Examples

## Not run: 
#load input in qtl2 zip format
load_input_and_run_cape("cross_file.zip")

#load input in qtl csv format
load_input_and_run_cape("cross_file.csv")

## End(Not run)


[Package cape version 3.1.0 Index]