EpitopePrioritization: Epitope prioritization based on immunogenicity scores and...

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

Epitope prioritization based on immunogenicity scores and escape potentials.

Description

Epitope prioritization based on immunogenicity scores and escape potentials.

Usage

EpitopePrioritization(
  featureDF,
  metadataDF,
  peptideSet,
  peptideLengthSet = 8:11,
  fragLib,
  aaIndexIDSet = "all",
  fragLenSet = 3:8,
  fragDepth = 10000,
  fragLibType = "Weighted",
  featureSet = NULL,
  seedSet = 1:5,
  coreN = parallel::detectCores(logical = F),
  outDir = paste0("./Output_", format(Sys.time(), "%Y.%m.%d.%H.%M.%S"))
)

Arguments

featureDF	A pre-computed feature dataframe for model construction.
metadataDF	A metadata dataframe, consisting only of "Peptide" and "Immunogenicity" columns, for model construction.
peptideSet	A set of new peptide sequences.
peptideLengthSet	A set of allowed amino acid sequence lengths. Peptides not falling in this range will be discarded.
fragLib	Either the dataframe of fragment libraries generated by CPP_FragmentLibrary or the path to the fst file.
aaIndexIDSet	A set of AAIndex IDs indicating the AACP scales to be used. Set "all" to shortcut the selection of all available AACP scales.
fragLenSet	A set of sliding window sizes.
fragDepth	A fragment library size. Must be an integer vector of length one.
fragLibType	A string indicating the types of fragment libraries to be used. Must be a character vector of length one.
featureSet	A minimum set of features. Combinations of fragment lengths and AAIndex IDs are internally extracted for calculating CPPs.
seedSet	A set of random seeds.
coreN	The number of cores to be used for parallelization.
outDir	Destination directory to save the results.

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