default_params_doc {netmhc2pan}

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,
  netmhc2pan_archive_filename,
  netmhc2pan_bin_tarfile_path,
  netmhc2pan_bin_url,
  netmhc2pan_data_tarfile_path,
  netmhc2pan_data_url,
  netmhc2pan_folder_name,
  netmhc2pan_subfolder,
  netmhc2pan_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. DRB1_0101. See get_netmhc2pan_alleles for a full list

do_filter

set to TRUE if the results of NetMHCIIpan must be filtered

fasta_filename

the name of a FASTA file with protein sequences

folder_name

the folder to install NetMHCIIpan, which is "/home/[usename]/.local/share" by default

mhc_haplotype

one MHC haplotype, e.g. DRB1_0101. See get_netmhc2pan_alleles for a full list

netmhc2pan_archive_filename

the NetMHC2pan archive filename, for example netMHCIIpan-3.2.Linux.tar.gz, which is used in installation of NetMHC2pan. Use get_netmhc2pan_archive_filename to get this filename.

netmhc2pan_bin_tarfile_path

path of the NetMHCIIpan binary tarball file

netmhc2pan_bin_url

URL to download the NetMHCIIpan binary tarball file from, similar to, for example, https://www.cbs.dtu.dk/download/12345678-1234-1234-1234-123456789ABC. Use get_netmhc2pan_bin_url to get the default URL.

netmhc2pan_data_tarfile_path

path of the NetMHCIIpan data tarball file

netmhc2pan_data_url

URL to download the NetMHCIIpan data tarball file from, similar to, for example, https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/data.Linux.tar.gz. Use get_netmhc2pan_data_url to get the default URL.

netmhc2pan_folder_name

the folder (to be) used by NetMHCIIpan. From this location, a subfolder for NetMHCIIpan is created. Use get_default_netmhc2pan_folder to see the location of the default NetMHCIIpan folder. Use get_default_netmhc2pan_subfolder to see the location of the default NetMHCIIpan subfolder.

netmhc2pan_subfolder

the subfolder (to be) used by NetMHCIIpan. Use get_default_netmhc2pan_subfolder to see the location of the default NetMHCIIpan subfolder

netmhc2pan_version

the NetMHCIIpan version, for example 3.2. Use get_default_netmhc2pan_version to get the default NetMHCIIpan version

os

the operating system as obtained by rappdirs::app_dir()$os. netmhc2pan 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