check_mhc_haplotype_name: Check an MHC haplotype name

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

Check an MHC haplotype name

Description

Check an MHC haplotype name

Usage

check_mhc_haplotype_name(mhc_haplotype, ic50_prediction_tool)

Arguments

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.
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

Examples

library(bbbq)

# EpitopePrediction can only do MHC-I
check_mhc_haplotype_name(
  mhc_haplotype = get_mhc1_haplotypes()[1],
  ic50_prediction_tool = "EpitopePrediction"
)

if (netmhc2pan::is_netmhc2pan_installed()) {
  # NetMHCIIpan can only do MHC-II
  check_mhc_haplotype_name(
    mhc_haplotype = get_mhc2_haplotypes()[1],
    ic50_prediction_tool = "netmhc2pan"
  )
}

if (mhcnuggetsr::is_mhcnuggets_installed()) {

  #' # MHCnuggets can do both MHC-I and MHC-II
  check_mhc_haplotype_name(
    mhc_haplotype = get_mhc1_haplotypes()[1],
    ic50_prediction_tool = "mhcnuggetsr"
  )
  check_mhc_haplotype_name(
    mhc_haplotype = get_mhc2_haplotypes()[1],
    ic50_prediction_tool = "mhcnuggetsr"
  )
}

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