predict_ic50s: Predict the IC50s from a sequence

In tzina97/netMHCpanW: Interface to 'NetMHCpan'

Predict the IC50s from a sequence

Description

Predict the IC50s from a sequence

Usage

predict_ic50s(
  protein_sequence,
  peptide_length,
  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

protein_sequence	a protein sequence, for example FAMILYVW
peptide_length	length of a peptide
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 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.

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