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netmhc2pan (version 1.3.2)

predict_ic50s: Predict the IC50s from a sequence

Description

Predict the IC50s from a sequence

Usage

predict_ic50s(
  protein_sequence,
  peptide_length,
  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()
)

Value

a tibble with columns:

  • peptide the peptide fragment, each of length peptide_length

  • ic50 the predicted IC50 (in nM)

The number of rows equals protein_sequence - peptide_length + 1.

Arguments

protein_sequence

a protein sequence, for example FAMILYVW

peptide_length

length of a peptide

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