mhcnuggetsr (version 1.1)

default_params_doc: This function does nothing. It is intended to inherit the documentation of the parameters from.

Description

This function does nothing. It is intended to inherit the documentation of the parameters from.

Usage

default_params_doc(
  ba_models,
  folder_name,
  mhc,
  mhcs,
  mhc_class,
  mhcnuggets_options,
  mhcnuggets_url,
  n_aas,
  peptide,
  peptides,
  peptide_length,
  peptides_path,
  protein_sequence,
  verbose
)

Arguments

ba_models

Set to TRUE to use a pure BA model

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

mhc

the MHC haplotype name

mhcs

the MHC haplotype names

mhc_class

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

mhcnuggets_options

options to run MHCnuggets with, as can be created by create_mhcnuggets_options.

mhcnuggets_url

URL to the MHCnuggets GitHub repository

n_aas

number of amino acids

peptide

one peptide sequence

peptides

one of more peptide sequences

peptide_length

length of a peptide, in number of amino acids

peptides_path

the path to the peptides

protein_sequence

protein sequence, in uppercase, for example FAMILYVW

verbose

set to TRUE for more debug information