calc_p_det_tmh_mut: Calculate the chance that a TMH one-mutation mutant is...

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

Calculate the chance that a TMH one-mutation mutant is detected

Description

Calculate the chance that a TMH one-mutation mutant is detected

Usage

calc_p_det_tmh_mut(
  protein_sequence,
  mhc_haplotype,
  peptide_length,
  ic50_prediction_tool,
  n_adjancent_sequences = Inf,
  percentile = get_ic50_percentile_binder()
)

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
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
n_adjancent_sequences	look at the n_adjancent_sequences adjacent sequences, instead of all of them. The (maximum) number of adjacent sequences is 19 * peptide_length, where peptide_length is the peptide length in amino acids, and 19 in the number of possible amino acids to change to (as there are 20 different 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.

Author(s)

Richèl J.C. Bilderbeek

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