Table 2.

checknetMHCpan function parameters

Parameter	Description	Default value
netmhcpan_directory	the directory where netMHCpan is installed (i.e., ‘/usr/bin’ or ‘/usr/local/bin’, depending on where you have it installed)	No defaults. Necessary input.
netmhcpan_alleles	a vector composed of the alleles the peptides will be tested against.	No defaults. Necessary input.
peptide_rerun	the database search results from the second peaks run	No defaults. Necessary input.
HF_step1_output	the data frame from the HybridFinder function of the containing the spliced peptide potential explanations as well as RT, m/z, ALC, Scan & Fraction	No defaults. Necessary input.
(Optional) export_files : boolean (True or False)	by default it is set to False, however, if set to True, then the following input is essential.	FALSE
(Optional) export_dir	file path to the directory where the output files should be stored. This parameter is necessary for the export.	NULL