predict_ic50_from_file: Predict the half maximal inhibitory concentration (aka IC50)...

In richelbilderbeek/mhcnuggetsr: Call MHCnuggets

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"),
  verbose = FALSE
)

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.
verbose	set to TRUE for more debug information

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
  )
}

richelbilderbeek/mhcnuggetsr documentation built on Nov. 9, 2023, 10 p.m.