default_params_doc: This function does nothing. It is intended to inherit is...
In richelbilderbeek/ncbi_results: Creates Results

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(
  fasta_filename,
  fasta_filenames,
  folder_name,
  gene_ids_filename,
  gene_names_filename,
  is_in_tmh_filename,
  is_in_tmh_filenames,
  n_gene_ids,
  n_snps,
  ppoisbinom_plot_filename,
  results_filename,
  snps_filename,
  snps_filenames,
  snps_id_filename,
  snps_id_filenames,
  topo_filename,
  topo_filenames,
  use_color,
  use_transparency,
  variations_csv_filename,
  variations_csv_filenames,
  variations_rds_filename,
  variations_rds_filenames,
  verbose
)

Arguments

`fasta_filename`	name of a FASTA file with a protein sequence
`fasta_filenames`	name of one or more FASTA files with protein sequences
`folder_name`	name of the folder
`gene_ids_filename`	the filename to save the gene IDs to. For the experiment, use `gene_ids.csv`
`gene_names_filename`	the filename to save the gene IDs and gene names to, as can be read by read_gene_names_file. For the experiment, use `gene_names.csv`
`is_in_tmh_filename`	the filename to save the `is_in_tmh` table to (as can be read by read_is_in_tmh_file). For the experiment, use `[gene_name]_is_in_tmh.csv`
`is_in_tmh_filenames`	the filename to save the `is_in_tmh` tables to (each of which can be read by read_is_in_tmh_file). For the experiment, use `[gene_name]_is_in_tmh.csv`
`n_gene_ids`	the number of gene IDs. Use Inf to use all gene IDs
`n_snps`	the number of SNPs. Use Inf to use all SNS IDs
`ppoisbinom_plot_filename`	file to save the poisbinom plot to
`results_filename`	name of the results file. For the experiment, use `results.csv`
`snps_filename`	one filenames of a file containing the SNP IDs, named `[gene_name]_snps.csv`. These files can be read by read_snps_file
`snps_filenames`	one or more filenames of files containing the SNP IDs, named `[gene_name]_snps.csv`. These files can be read by read_snps_file
`snps_id_filename`	one filenames of a file containing the SNP IDs, named `[gene_name]_snps.csv`. These files can be read by read_snps_file
`snps_id_filenames`	one or more filenames of files containing the SNP IDs, named `[gene_name]_snps.csv`. These files can be read by read_snps_file
`topo_filename`	name of a `.topo` file with a protein topology
`topo_filenames`	name of one or more `.topo` files with protein topologies
`use_color`	set to TRUE to use color, set to FALSE for black-and-white
`use_transparency`	set to TRUE to use transparency. Useful when creating EPS, as these do not support transparency
`variations_csv_filename`	name of a `[gene_name]_variations.csv` file
`variations_csv_filenames`	names of one or more `[gene_name]_variations.csv` files
`variations_rds_filename`	name of a `[gene_name]_variations.rds` file
`variations_rds_filenames`	names of one or more `[gene_name]_variations.rds` files
`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