create_mhcnuggets_options {mhcnuggetsr}

Create a set of MHCnuggets options.

Description

Create a set of options to run MHCnuggets with.

Usage

create_mhcnuggets_options(
  mhc_class = NA,
  mhc,
  ba_models = FALSE,
  verbose = FALSE,
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

mhc_class

MHC class. Must be I, II or NA. Use NA to let the class be deduced automatically

mhc

the MHC haplotype name

ba_models

Set to TRUE to use a pure BA model

verbose

set to TRUE for more debug information

folder_name

superfolder of MHCnuggets. The name of the superfolder is /home/[user_name]/.local/share by default, as can be obtained byget_default_mhcnuggets_folder

mhcnuggets_url

URL to the MHCnuggets GitHub repository

Details

This function will give an error message if the arguments are invalid.

Value

an mhcnuggets_options

Note

an mhcnuggets_options created by create_mhcnuggets_options is always checked by check_mhcnuggets_options

Author(s)

Richèl J.C. Bilderbeek

See Also

use create_test_mhcnuggets_options to create an MHCnuggets object for testing

Examples

if (is_mhcnuggets_installed()) {
  create_mhcnuggets_options(
    mhc = "HLA-A02:01"
  )
}