default_params_doc: This function does nothing. It is intended to inherit the...

In richelbilderbeek/mhcnuggetsr: Call MHCnuggets

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,
  filename,
  mhc,
  mhcs,
  mhc_class,
  mhcnuggets_options,
  mhcnuggets_output_filename,
  mhcnuggets_url,
  mhcnuggetsr_folder,
  n_aas,
  ormr_folder_name,
  peptide,
  peptides,
  peptide_length,
  peptides_path,
  protein_sequence,
  verbose
)

Arguments

ba_models	Set to TRUE to use a pure BA model
filename	name of a file
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_output_filename	name of a temporary file where MHCnuggets writes its output to
mhcnuggets_url	URL to the MHCnuggets GitHub repository
mhcnuggetsr_folder	folder where mhcnuggetsr stores its temporary files. Use get_default_mhcnuggetsr_folder for its default value.
n_aas	number of amino acids
ormr_folder_name	folder used by the ormr package to install Python packages to. Use python3 to install Python packages via pip. Default value is python3
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

Note

This is an internal function, so it should be marked with @noRd. This is not done, as this will disallow all functions to find the documentation parameters

Author(s)

Richèl J.C. Bilderbeek

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