predict_ic50s {mhcnuggetsr}

Predict the half maximal inhibitory concentrations (aka IC50s) (in nM) of all possible n-mers within a peptide

Description

Predict the half maximal inhibitory concentrations (aka IC50s) (in nM) of all possible n-mers within a peptide

Usage

predict_ic50s(
  protein_sequence,
  peptide_length,
  mhcnuggets_options,
  peptides_path = create_temp_peptides_path()
)

Arguments

protein_sequence

protein sequence, in uppercase, for example FAMILYVW

peptide_length

length of a peptide, in number of amino acids

mhcnuggets_options

options to run MHCnuggets with, as can be created by create_mhcnuggets_options.

peptides_path

the path to the peptides

Value

a tibble with columns:

• peptide the peptide fragment, each of length peptide_length

• ic50 the predicted IC50 (in nM)

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {

  mhcnuggets_options <- create_mhcnuggets_options(
    mhc = "HLA-A02:01"
  )

  predict_ic50s(
    protein_sequence = "AIAACAMLLVCCCCCC",
    peptide_length = 13,
    mhcnuggets_options = mhcnuggets_options
  )
}