default_params_doc: This function does nothing. It is intended to inherit is...
In richelbilderbeek/nmhc2ppreds: netmhc2pan Predictions

Description Usage Arguments Note Author(s)

This function does nothing. It is intended to inherit is parameters' documentation.

default_params_doc(
  binding_strength_threshold,
  fasta_filename,
  haplotype,
  haplotypes,
  haplotype_id,
  haplotype_ids,
  ic50_threshold,
  max_hydrophobicity,
  mhc_haplotype,
  min_hydrophobicity,
  n_peptides,
  peptide_length,
  protein_sequence,
  protein_sequences,
  verbose
)

`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
`fasta_filename`	name of a FASTA file
`haplotype`	the netmhc2pan haplotype ID, for example `HLA-A33:01`. Use get_haplotype_lut to get a lookup table that maps a `nmhc2ppreds` haplotype ID to an netmhc2pan haplotype name
`haplotypes`	one ore more netmhc2pan haplotype IDs, for example `HLA-A33:01`. Use get_haplotype_lut to get a lookup table that maps a `nmhc2ppreds` haplotype ID to an netmhc2pan haplotype name
`haplotype_id`	the `nmhc2ppreds` haplotype ID, for example `h1`. Use get_haplotype_lut to get a lookup table that maps a `nmhc2ppreds` haplotype ID to an netmhc2pan haplotype name
`haplotype_ids`	one or more `nmhc2ppreds` haplotype IDs, for example `h1`. Use get_haplotype_lut to get a lookup table that maps a `nmhc2ppreds` haplotype ID to an netmhc2pan haplotype name
`ic50_threshold`	peptides with a predicted IC50 value (in nM) lower than this will be considered binders. A threshold of 500 (nM) is common.
`max_hydrophobicity`	the maximal hydrophobicity
`mhc_haplotype`	haplotype of either HMC-I or MHC-II. in netmhc2panr format. Use `netmhc2panr::get_mhc_1_haplotypes` to get a list of all MHC-I haplotypes. Use `netmhc2panr::get_mhc_2_haplotypes` to get a list of all MHC-II haplotypes.
`min_hydrophobicity`	the minimal hydrophobicity
`n_peptides`	number of peptides
`peptide_length`	length of the peptide in amino acids
`protein_sequence`	a protein sequence
`protein_sequences`	one or more protein sequences
`verbose`	set to TRUE for more output

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

Richèl J.C. Bilderbeek

richelbilderbeek/nmhc2ppreds documentation built on Aug. 21, 2021, 10:45 a.m.