get_ic50s_lut: Get a lookup table for IC50 predictions of epitopes

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

Get a lookup table for IC50 predictions of epitopes

Description

Get a lookup table for IC50 predictions of epitopes. This lookup table is read from file. If a needed file is absent, it will be downloaded. For the human reference proteome, each table is approx 300 megabytes.

Usage

get_ic50s_lut(
  target_name,
  haplotype,
  peptide_length,
  ic50_prediction_tool,
  verbose = FALSE
)

Arguments

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.
haplotype	one MHC-I or MHC-II haplotype
peptide_length	length of the peptide in amino acids
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
verbose	set to TRUE for more output

Details

The scripts that created these look-up tables are at by https://github.com/richelbilderbeek/bbbq_article_issue_167

richelbilderbeek/bbbq documentation built on July 27, 2023, 2:15 a.m.