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

In richelbilderbeek/tmhmm: Interface to TMHMM

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(
  download_url,
  fasta_filename,
  fasta_text,
  folder_name,
  locatome,
  one_protein_fasta_filename,
  protein_sequence,
  protein_sequences,
  temp_fasta_filename,
  temp_topology_filename,
  tmhmm_bin_filename,
  tmhmm_filename,
  tmhmm_result,
  topology,
  topology_sequence,
  topology_sequences,
  topology_text,
  verbose
)

Arguments

download_url	the URL to download TMHMM from
fasta_filename	path to a FASTA file
fasta_text	the content of a FASTA file as text, for example c(">Protein 1", "FAMILYVW")
folder_name	superfolder of TMHMM. The superfolder's name is /home/[user_name]/.local/share by default, as can be obtained by get_default_tmhmm_folder
locatome	text similar to a FASTA file, with protein names and the locations of its amino acids
one_protein_fasta_filename	name of a FASTA file, that contains one name and one sequence
protein_sequence	a protein sequence
protein_sequences	one or more protein sequences
temp_fasta_filename	filename to temporarily save the protein names and sequences. This file will be deleted when this function completed successfully
temp_topology_filename	filename to temporarily save the topology. This file will be deleted when this function completed successfully
tmhmm_bin_filename	path to the TMHMM binary file. Its default path can be ontained by using get_default_tmhmm_bin_path
tmhmm_filename	filename to write the TMHMM results to
tmhmm_result	the results of a call to TMHMM, for example, c(">protein name", "ooooMMMMiiiii")
topology	a tibble with two columns, named name for a protein's name and topology, for its predicted topology (e.g. ooooMMMMiiiii).
topology_sequence	a topology sequence, for example "iiiimmmmmoooo"
topology_sequences	one or more topology sequences, for example c("iiiimmmmooooo", "iiiii")
topology_text	the topology as text, that alternates protein names and topology sequences. This is the same form as a FASTA file, for example c(">Protein A", "iiiimmmmmoooo")
verbose	set to TRUE for more output

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/tmhmm documentation built on Sept. 3, 2022, 5:14 p.m.