default_params_doc: This function does nothing. It is intended to inherit is...
In pureseqtmr: Predict Transmembrane Protein Topology

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(
  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