tmhmm (version 1.3)

default_params_doc: 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,
  folder_name,
  locatome,
  protein_sequence,
  protein_sequences,
  tmhmm_bin_filename,
  tmhmm_filename,
  tmhmm_result,
  topology,
  verbose
)

Arguments

download_url

the URL to download TMHMM from

fasta_filename

path to a FASTA file

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

protein_sequence

a protein sequence

protein_sequences

one or more protein sequences

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).

verbose

set to TRUE for more output