default_params_doc: This function does nothing. It is intended to inherit is...
In netmhc2pan: Interface to 'NetMHCIIpan'

default_params_doc

R Documentation

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