default_params_doc: Documentation of general function arguments. This function...
In richelbilderbeek/cobaltr: Interface Io COBALT

default_params_doc

R Documentation

Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.

Description

Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.

Usage

default_params_doc(
  cobalt_folder,
  cobalt_options,
  conserved_domain_threshold,
  conservation_score_threshold,
  conserved_block_filename,
  dfb_added_weight,
  destination_filename,
  do_dry_run,
  domain_database_filename,
  fasta_filename,
  ffb_added_weight,
  filler_threshold,
  middle_extend_gap_penalty,
  no_rps,
  open_gap_in_middle_penalty,
  pac_filename,
  pseudocount_constant,
  residue_frequencies_filename,
  score_matrix_name,
  search_around_ccs,
  search_pattern_filename,
  terminal_extend_gap_penalty,
  terminal_open_gap_penalty,
  use_fastme,
  verbose
)

Arguments

`cobalt_folder`	the folder where COBALT is installed in. Use get_default_cobalt_folder to get the default COBALT folder
`cobalt_options`	a set of COBALT options, as can be created by create_cobalt_options
`conserved_domain_threshold`	the threshold of the E-value for selecting conserved domains. The COBALT `-evalue` flag
`conservation_score_threshold`	the minimum average score needed for a multiple alignment column to be considered as conserved. The COBALT `-ccc` flag
`conserved_block_filename`	filename containing conserved blocks, the COBALT `-b` option
`dfb_added_weight`	the amount of extra weight (0..1) to give the actual sequence letter at that position, The COBALT `-dfb` flag
`destination_filename`	filename for destination text seqalign the COBALT `-seqalign` option
`do_dry_run`	Do a dry run, that is, only test all preconditions The COBALT `-dryrun` flag
`domain_database_filename`	domain database filename, the COBALT `-db` option
`fasta_filename`	name of a FASTA file
`ffb_added_weight`	the amount of extra weight (0..1) to give the actual sequence letter at that position when assigning filler residue frequencies. The COBALT `-ffb` flag
`filler_threshold`	the threshold of the E-value for aligning filler segments. The COBALT `-evalue2` flag
`middle_extend_gap_penalty`	The COBALT `-e1` flag
`no_rps`	do not perform initial RPS blast search The COBALT `-norps` flag
`open_gap_in_middle_penalty`	The COBALT `-g1` flag
`pac_filename`	name of the file containing pairwise alignment constraints, one per line, each of the following form: `seq1_idx seq1_start seq1_end seq2_idx seq2_start seq2_end`. The COBALT `-c` flag
`pseudocount_constant`	the pseudocount constant The COBALT `-pseudo` flag
`residue_frequencies_filename`	filename containing residue frequencies, the COBALT `-f` option
`score_matrix_name`	name of the COBALT score matrix. Use get_matrix_names to get a list of all possible matrix names
`search_around_ccs`	look for conserved columns and iterate if any are found. The COBALT `-iter` flag
`search_pattern_filename`	filename containing search patterns, the COBALT `-p` option
`terminal_extend_gap_penalty`	The COBALT `-e0` flag
`terminal_open_gap_penalty`	the gap open penalty for initial/terminal gaps. The COBALT `-g0` flag
`use_fastme`	use FastME tree generation algorithm (instead of neighbor joining). The COBALT `-fastme` flag
`verbose`	verbose output the COBALT `-v` option

Note

This is an internal function, so it should be marked with @export. This is not done, as this will disallow all functions to find the documentation parameters