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

In tzina97/netMHCpanW: Interface to 'NetMHCpan'

This function does nothing. It is intended to inherit is parameters' documentation.

Description

This function does nothing. It is intended to inherit is parameters' documentation.

Usage

default_params_doc(
  alleles,
  do_filter,
  fasta_filename,
  folder_name,
  mhc_haplotype,
  netmhcpan_archive_filename,
  netmhcpan_bin_tarfile_path,
  netmhcpan_bin_url,
  netmhcpan_data_tarfile_path,
  netmhcpan_data_url,
  netmhcpan_folder_name,
  netmhcpan_subfolder,
  netmhcpan_version,
  os,
  peptide_length,
  peptides,
  protein_sequence,
  temp_fasta_filename,
  temp_local_file,
  temp_xls_filename,
  verbose,
  xls_filename
)

Arguments

alleles	one or more alleles, e.g. HLA-A0101. See get_netmhcpan_alleles for a full list
do_filter	set to TRUE if the results of NetMHCpan must be filtered
fasta_filename	the name of a FASTA file with protein sequences
folder_name	the folder to install NetMHCpan, which is "/home/[usename]/.local/share" by default
mhc_haplotype	one MHC haplotype, e.g. HLA-A0101. See get_netmhcpan_alleles for a full list
netmhcpan_archive_filename	the NetMHCpan archive filename, for example netMHCpan-4.1b.Linux.tar.gz, which is used in installation of NetMHCpan. Use get_netmhcpan_archive_filename to get this filename.
netmhcpan_bin_tarfile_path	path of the NetMHCpan binary tarball file
netmhcpan_bin_url	URL to download the NetMHCpan binary tarball file from, similar to, for example, FIX LINK. Use get_netmhcpan_bin_url to get the default URL.
netmhcpan_data_tarfile_path	path of the NetMHCpan data tarball file
netmhcpan_data_url	URL to download the NetMHCpan data tarball file from, similar to, for example, https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/data.tar.gz Use get_netmhcpan_data_url to get the default URL.
netmhcpan_folder_name	the folder (to be) used by NetMHCpan. From this location, a subfolder for NetMHCpan is created. Use get_default_netmhcpan_folder to see the location of the default NetMHCpan folder. Use get_default_netmhcpan_subfolder to see the location of the default NetMHCpan subfolder.
netmhcpan_subfolder	the subfolder (to be) used by NetMHCpan. Use get_default_netmhcpan_subfolder to see the location of the default NetMHCpan subfolder
netmhcpan_version	the NetMHCpan version, for example 4.1. Use get_default_netmhcpan_version to get the default NetMHCpan version
os	the operating system as obtained by rappdirs::app_dir()$os. netmhcpan supports Linux ('unix') only
peptide_length	length of a peptide
peptides	one or more peptide sequences
protein_sequence	a protein sequence, for example FAMILYVW
temp_fasta_filename	name for a temporary FASTA file, which will be deleted automatically
temp_local_file	path to the temporary file to store the URL to. This file will be deleted afterwards.
temp_xls_filename	name for a temporary xls file, which will be deleted automatically
verbose	set to TRUE for more output
xls_filename	name of an xls file

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

tzina97/netMHCpanW documentation built on April 26, 2022, 1:18 a.m.