predict_ic50 {mhcnuggetsr}

Predict the IC50 for peptides.

Description

Predict the half maximal inhibitory concentration (aka IC50) (in nM) for one or more peptides. Each peptide must be 15 amino acids at most (use predict_ic50s to predict the IC50s for longer peptides)

Usage

predict_ic50(
  mhcnuggets_options,
  peptides,
  peptides_path = create_temp_peptides_path()
)

Arguments

mhcnuggets_options

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

peptides

one of more peptide sequences

peptides_path

the path to the peptides

Value

a tibble with two columns: (1) peptide, which holds the peptide sequence, and (2) ic50, which holds the predicted IC50

Note

this function uses a temporary file, because MHCnuggets reads its input from file. This temporary file is deleted after this function passed successfully.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {

  peptides <- c("AIAACAMLLV", "ALVCYIVMPV", "ALEPRKEIDV")
  mhc_1_haplotype <- "HLA-A02:01"

  mhcnuggets_options <- create_mhcnuggets_options(
    mhc = mhc_1_haplotype
  )

  predict_ic50(
    peptides = peptides,
    mhcnuggets_options = mhcnuggets_options
  )
}