predict_ic50: Predict the IC50 for peptides.

In tzina97/netMHCpanW: Interface to 'NetMHCpan'

Predict the IC50 for peptides.

Description

Predict the half maximal inhibitory concentration (aka IC50) (in nM) for one or more peptides, where the peptides are used as-is, instead of split into smaller peptides. Each peptide must be 15 amino acids at most (use predict_ic50s to predict the IC50s for longer peptides)

Usage

predict_ic50(
  peptides,
  mhc_haplotype,
  netmhcpan_folder_name = get_default_netmhcpan_folder(),
  temp_fasta_filename = netmhcpan::create_temp_fasta_filename(),
  temp_xls_filename = netmhcpan::create_temp_xls_filename()
)

Arguments

peptides	one or more peptide sequences
mhc_haplotype	one MHC haplotype, e.g. HLA-A0101. See get_netmhcpan_alleles for a full list
netmhcpan_folder_name	the folder (to be) used by NetMHCpan. From this location, a subfolder for NetMHCpan is created. Use get_default_netmhcpan_folder to see the location of the default NetMHCpan folder. Use get_default_netmhcpan_subfolder to see the location of the default NetMHCpan subfolder.
temp_fasta_filename	name for a temporary FASTA file, which will be deleted automatically
temp_xls_filename	name for a temporary xls file, which will be deleted automatically

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 NetMHCpan reads its input from file. This temporary file is deleted after this function passed successfully.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_netmhcpan_installed()) {

  predict_ic50(
    peptides = c("AIAACAMLLV", "ALVCYIVMPV"),
    mhc_haplotype = "HLA-A0101"
  )
}

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