are_detected: Are the protein sequences detected by either MHC-I or MHC-II?

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

Are the protein sequences detected by either MHC-I or MHC-II?

Description

Are the protein sequences detected by either MHC-I or MHC-II?

Usage

are_detected(
  protein_sequences,
  mhc_haplotype,
  peptide_length,
  percentile = get_ic50_percentile_binder(),
  ic50_prediction_tool
)

Arguments

protein_sequences	one or more protein sequences
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.
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.
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

Author(s)

Richèl J.C. Bilderbeek

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