ContactPotentialProfiling_FragmentLibrary: Generate sequence fragment libraries.

In masato-ogishi/Repitope: Epitope immunogenicity prediction through in silico TCR-peptide contact potential profiling

Generate sequence fragment libraries.

Description

CPP_FragmentLibrary generates a formatted fragment library datatable.

Usage

CPP_FragmentLibrary(
  tcrSequenceSet,
  fragLenSet = 3:8,
  maxFragDepth = 1e+05,
  seedSet = 1:5,
  coreN = parallel::detectCores(logical = F),
  tmpDir = file.path(tempdir(), "FragLibDT", format(Sys.time(),
    "%Y.%m.%d.%H.%M.%S"))
)

Arguments

tcrSequenceSet	A set of TCR CDR3B amino acid sequences.
fragLenSet	A set of sliding window sizes.
maxFragDepth	The maximum depth of fragments used to compute repertoire-wide TCR-peptide contact potentials.
seedSet	A set of random seeds.
coreN	The number of cores to be used for parallelization.
tmpDir	Destination directory to save intermediate files.

masato-ogishi/Repitope documentation built on Feb. 14, 2023, 5:47 a.m.