default_params_doc {pureseqtmr}

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_file_text,
  folder_name,
  protein_sequence,
  protein_sequences,
  pureseqtm_filename,
  pureseqtm_proteome_text,
  pureseqtm_result,
  pureseqtm_url,
  temp_fasta_filename,
  temp_folder_name,
  tmhmm_topology,
  topology,
  topology_filename,
  topology_str,
  topology_strs,
  verbose
)

Arguments

download_url

the URL to download PureseqTM from

fasta_filename

path to a FASTA file

fasta_file_text

text of a FASTA file

folder_name

superfolder of PureseqTM. The superfolder's name is /home/[user_name]/.local/share by default, as can be obtained by get_default_pureseqtm_folder

protein_sequence

a protein sequence, with the amino acids as capitals, for example MEILCEDNTSLSSIPNSL. Use check_protein_sequence to check if a protein sequence is valid.

protein_sequences

one ore more protein sequence, each sequence with the amino acids as capitals, for example MEILCEDNTSLSSIPNSL

pureseqtm_filename

filename to write the PureseqTM results to

pureseqtm_proteome_text

the output of a call to PureseqTM_proteome.sh

pureseqtm_result

the result of a PureseqTM run

pureseqtm_url

URL of the PureseqTM git repository

temp_fasta_filename

temporary FASTA filename, which will deleted after usage

temp_folder_name

path of a temporary folder. The folder does not need to exist. Files that are out in this folder are not automatically deleted, which is not a problem, as the default path given by tempdir is automatically cleaned by the operating system

tmhmm_topology

topology as used by TMHMM

topology

the topology as a tibble with the columns 'name' and 'topology', where the 'name' column hold all the proteins' names, and 'topology' contains the respective topologies as strings.

topology_filename

name of the file to save a protein's topology to

topology_str

the topology as a string, for example 000000111100000

topology_strs

the topologies as zero, one oor more strings, for example c("0", "1")

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