predict_ic50 {netmhc2pan}

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,
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  temp_fasta_filename = netmhc2pan::create_temp_fasta_filename(),
  temp_xls_filename = netmhc2pan::create_temp_xls_filename()
)

Arguments

peptides

one or more peptide sequences

mhc_haplotype

one MHC haplotype, e.g. DRB1_0101. See get_netmhc2pan_alleles for a full list

netmhc2pan_folder_name

the folder (to be) used by NetMHCIIpan. From this location, a subfolder for NetMHCIIpan is created. Use get_default_netmhc2pan_folder to see the location of the default NetMHCIIpan folder. Use get_default_netmhc2pan_subfolder to see the location of the default NetMHCIIpan 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 NetMHC2pan reads its input from file. This temporary file is deleted after this function passed successfully.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_netmhc2pan_installed()) {

  predict_ic50(
    peptides = c("AIAACAMLLV", "ALVCYIVMPV"),
    mhc_haplotype = "DRB1_0416"
  )
}