In tzina97/netMHCpanW: Interface to 'NetMHCpan'

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

This demo shows how to predict the binding strength of peptides to different Major Histocompatibility MHC haplotypes.

First load the library:

library(netmhcpan)

This demo assumes NetMHCpan is installed. Installation cannot be done netmhcpan, as one needs to request a download link at http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan/.

To install netMHCpan, use install_netmhcpan with the download link:

install_netmhcpan(" ")

The installation of netmhcpan is checked, with the goal of producing a helpful error message:

tryCatch(
  check_netmhcpan_installation(),
  error = function(e) print(e)
)

Now, lets use the sequence of an example protein:

sequence <- "FAMILYVWFAMILYV"
message(sequence)

Now, we need to select an MHC haplotype. There are many alleles, so first we count the number of haplotypes:

if (is_netmhcpan_installed()) {
  mhc_haplotypes <- get_netmhcpan_alleles()
  length(mhc_haplotypes)
}

Now, we simply pick the first haplotype:

if (is_netmhcpan_installed()) {
  mhc_haplotype <- mhc_haplotypes[1]
}

Now, we can predict how strong our peptide binds to our allele, by obtaining the Inhibitory Concentration 50% (IC50) value in nanomolars (nM), of which lower values indicate stronger binders:

if (is_netmhcpan_installed()) {
  knitr::kable(
    predict_ic50(
      peptides = sequence,
      mhc_haplotype = mhc_haplotype
    )
  )

}

To investigate if whole a protein is immunogenic, we need to obtain the IC50 values for all its cleaved products. As the MHC-I molecules prefers 13 amino acids residues, we can get the IC50 values for each residue as such:

if (is_netmhcpan_installed()) {
  knitr::kable(
    predict_ic50s(
      protein_sequence = "AVLWAGVAFLAFLQLTALVLNLL",
      peptide_length = 13,
      mhc_haplotype = mhc_haplotype
    )
  )

}

tzina97/netMHCpanW documentation built on April 26, 2022, 1:18 a.m.