run_netmhc2pan {netmhc2pan}

Run NetMHCIIpan

Description

Run NetMHCIIpan

Usage

run_netmhc2pan(
  fasta_filename,
  alleles = "DRB1_0101",
  peptide_length = 15,
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  temp_xls_filename = netmhc2pan::create_temp_xls_filename()
)

Arguments

fasta_filename

the name of a FASTA file with protein sequences

alleles

one or more alleles, e.g. DRB1_0101. See get_netmhc2pan_alleles for a full list

peptide_length

length of a peptide

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_xls_filename

name for a temporary xls file, which will be deleted automatically

Value

a data frame with the NetMHCIIpan results

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_netmhc2pan_installed()) {

  fasta_filename <- system.file(
    "extdata", "example.fasta", package = "netmhc2pan"
  )
  run_netmhc2pan(fasta_filename)

  # Two alleles
  alleles <- c("DRB1_0101", "DRB1_0102")
  # Run NetMHCpan with these two alleles
  run_netmhc2pan(fasta_filename, alleles = alleles)
}