default_params_doc: This function does nothing. It is intended to inherit is...
In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

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(
  binding_strength_threshold,
  data_folder,
  epitopeome_filename,
  fasta_filename,
  haplotype,
  haplotypes,
  hydrophobe_control_peptides_as_data_filename,
  ic50_prediction_tool,
  ic50_threshold,
  keep_selenoproteins,
  kyte_doolittle_scale_as_data_filename,
  max_hydrophobicity,
  mhc_class,
  mhc_haplotype,
  mhc_1_haplotype,
  mhc_2_haplotype,
  mhcnuggetsr_peptides_path,
  min_hydrophobicity,
  msa_method,
  msa_subst_matrix,
  n_peptides,
  non_tmh_eluted_filename,
  peptide,
  peptides,
  peptide_length,
  percentile,
  png_filename,
  protein_lengths_filename,
  protein_sequence,
  protein_sequences,
  proteome_filename,
  proteome_as_data_filename,
  proteome_9mer_hydrophobicity_as_data_filename,
  proteome_type,
  pureseqtmr_filename,
  target_name,
  tmh_9mers_as_data_filename,
  tmh_eluted_filename,
  tmh_overlapping_binders_as_data_filename,
  topology,
  topology_prediction_tool,
  transition_matrix,
  transition_matrix_name,
  trans_membrane_analysis_filename,
  triplet,
  verbose
)

Arguments

`binding_strength_threshold`	threshold of the MHC2 allele's binding strength. A low threshold, e.g. `5.0`, selects for the top 5 percent best binders
`data_folder`	folder where BBBQ stores its data, such as proteomes and prediced topologies.
`epitopeome_filename`	name of the file to store the epitopeome output. By default, this filename is generated by tempfile, and will be put in the `/tmp` folder, which is cleaned by the operating system
`fasta_filename`	name of a FASTA file
`haplotype`	one MHC-I or MHC-II haplotype
`haplotypes`	a list of MHC-I or MHC-II haplotypes
`hydrophobe_control_peptides_as_data_filename`	filename that stores hydrophobe control peptides as R data, for example 'work/hydrophobe-control-peptides.Rdata'
`ic50_prediction_tool`	tool to predict the IC50 from a peptide. Possible values are: mhcnuggetsr mhcnuggetsr, which uses MHCnuggets mhcnuggetsr netmhc2pan, which uses NetMHC2pam EpitopePrediction uses `EpitopePrediction`
`ic50_threshold`	peptides with a predicted IC50 value (in nM) lower than this will be considered binders. A threshold of 500 (nM) is common.
`keep_selenoproteins`	keep the selenoproteins. The reason to discard these, is that TMHMM cannot deal with selenoproteins.
`kyte_doolittle_scale_as_data_filename`	filename that stores the Kyte-Doolittle scale of hydrophobicity, for example 'data/kyte.doolittle.scale.Rdata'
`max_hydrophobicity`	the maximal hydrophobicity
`mhc_class`	the MHC class, for example `1`
`mhc_haplotype`	haplotype of either HMC-I or MHC-II. Use get_mhc1_haplotypes to get a list of all MHC-I haplotypes. Use get_mhc2_haplotypes to get a list of all MHC-II haplotypes.
`mhc_1_haplotype`	HMC-I haplotope. Use get_mhc1_haplotypes to get a list of all haplotypes
`mhc_2_haplotype`	HMC-II haplotope. Use get_mhc2_haplotypes to get a list of all haplotypes
`mhcnuggetsr_peptides_path`	path to a temporary file to create peptides, as needed by mhcnuggetsr, which is create_temp_peptides_path by default
`min_hydrophobicity`	the minimal hydrophobicity
`msa_method`	the `method` argument of msa. Valid methods are `ClustalW`, `ClustalOmega` (preferred for proteins) and `Muscle`
`msa_subst_matrix`	multiple sequence alignment substitution matrix, the `substitutionMatrix` argument of msa. For a protein alignment, relevant values are `blosum`, `pam` and `gonnet`
`n_peptides`	number of peptides
`non_tmh_eluted_filename`	Filename for the non-TMHs found on B-cells, for example 'data/non-TMH-Bcell-elution.txt'
`peptide`	peptide sequence, for example, `ARNDCQEV`
`peptides`	one ore more peptide sequences
`peptide_length`	length of the peptide in amino acids
`percentile`	how low the IC50 must be for the protein to be considered a binder. For example, 0.02 denotes that the protein must have an IC50 in the lowest 2 percent range. The default value is returned by get_ic50_percentile_binder.
`png_filename`	name of a PNG file
`protein_lengths_filename`	filename to store the length of all proteins in proteome, for example 'work/protein-lengths.txt'
`protein_sequence`	a protein sequence
`protein_sequences`	one or more protein sequences
`proteome_filename`	name of the file the proteome will be stored at
`proteome_as_data_filename`	filename to store the proteome in R data format, for example 'work/proteome.Rdata'
`proteome_9mer_hydrophobicity_as_data_filename`	filename to store the proteome 9-mer hydrophobicities in R data format, for example 'work/proteome.9mer.hydrophobicity.Rdata'
`proteome_type`	type of proteome, must be either `full` or `representative`
`pureseqtmr_filename`	name of the file to store the PureseqTM output. By default, this filename is generated by tempfile, and will be put in the `/tmp` folder, which is cleaned by the operating system `mhcn` for mhcnuggetsr
`target_name`	abbreviated name of organism or virus. Use get_target_names to get the valid values. Use get_target_english_name to get the English name of a target.
`tmh_9mers_as_data_filename`	filename to store per TMH protein, the indices at which it is TMH, in R data format. for example 'work/tmh.9mers.Rdata'
`tmh_eluted_filename`	Filename for the TMHs found on B-cells, for example, 'data/TMH-Bcell-elution.txt'
`tmh_overlapping_binders_as_data_filename`	filename to store per TMH overlapping binders in R data format. for example 'work/tmh-overlapping-binders.Rdata'
`topology`	a topology, as created by predict_topology
`topology_prediction_tool`	tool to predict the topology of a membrane protein. Possible values are: mhcnuggetsr pureseqtmr, which uses PureseqTM mhcnuggetsr tmhmm, which uses TMHMM
`transition_matrix`	the amino acid transition matrix, for example, the BLOSUM62 transition matrix as returned by get_aa_transition_matrix
`transition_matrix_name`	the name of an amino acid transition matrix, for example, `BLOSUM62`
`trans_membrane_analysis_filename`	Filename for uhhh, something, for example 'tmh-predictions/trans-membrane-analysis-shortened.txt'
`triplet`	a DNA triplet
`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