create_test_mhcnuggets_options: Create testing options for MHCnuggets

In richelbilderbeek/mhcnuggetsr: Call MHCnuggets

Create testing options for MHCnuggets

Description

Create a set of testing options to run MHCnuggets with. The most important setting is the use of a specific haplotype.

Usage

create_test_mhcnuggets_options(
  mhc_class = NA,
  mhc = "HLA-A02:01",
  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'

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {
  create_test_mhcnuggets_options()
}

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