is_detected: Determine if the haplotype has at least one binder to the...

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

Determine if the haplotype has at least one binder to the peptide

Description

Determine if the haplotype has at least one binder to the peptide

Usage

is_detected(
  protein_sequence,
  mhc_haplotype,
  peptide_length,
  percentile = get_ic50_percentile_binder(),
  ic50_prediction_tool
)

Arguments

protein_sequence	a protein sequence
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.