predict_ic50_from_file {mhcnuggetsr}

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

Description

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

Usage

predict_ic50_from_file(
  mhcnuggets_options,
  peptides_path,
  mhcnuggets_output_filename = mhcnuggetsr::create_temp_peptides_path(fileext = ".csv")
)

Arguments

mhcnuggets_options

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

peptides_path

the path to the peptides

mhcnuggets_output_filename

path to a temporary file to write the MHCnuggets results to. This file will be deleted at the end of the function if it passes successfully.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {

  peptides_path <- get_example_filename("test_peptides.peps")
  mhc_1_haplotype <- "HLA-A02:01"
  mhcnuggets_options <- create_mhcnuggets_options(
    mhc = mhc_1_haplotype
  )

  predict_ic50_from_file(
    peptides_path = peptides_path,
    mhcnuggets_options = mhcnuggets_options
  )
}