predict_ic50s: Predict the IC50s from a sequence

In netmhc2pan: Interface to 'NetMHCIIpan'

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()
)

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

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.

netmhc2pan documentation built on Nov. 9, 2023, 1:08 a.m.