create_mhcnuggets_options: Create a set of MHCnuggets options.

In richelbilderbeek/mhcnuggetsr: Call MHCnuggets

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,
  mhcnuggetsr_folder = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url(),
  folder_name = "deprecated"
)

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
mhcnuggetsr_folder	folder where mhcnuggetsr stores its temporary files. Use get_default_mhcnuggetsr_folder for its default value.
mhcnuggets_url	URL to the MHCnuggets GitHub repository
folder_name	deprecated name for 'mhcnuggetsr_folder'

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"
  )
}

richelbilderbeek/mhcnuggetsr documentation built on Nov. 9, 2023, 10 p.m.