Features: Feature computation.

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

Feature computation.

Description

Features_PeptDesc computes peptide descriptors.
Features_CPP computes descriptive statistics of TCR repertoire-wide contact potential distributions.
Features is a wrapper function.

Usage

Features_PeptDesc(
  peptideSet,
  fragLenSet = 3:8,
  featureSet = NULL,
  coreN = parallel::detectCores(logical = F)
)

Features_CPP(
  peptideSet,
  fragLib,
  aaIndexIDSet = "all",
  fragLenSet = 3:8,
  fragDepth = 10000,
  fragLibType = c("Deduplicated", "Weighted", "Mock"),
  featureSet = NULL,
  seedSet = 1:5,
  coreN = parallel::detectCores(logical = F),
  tmpDir = file.path(tempdir(), "FeatureDF", format(Sys.time(),
    "%Y.%m.%d.%H.%M.%S"))
)

Features(
  peptideSet,
  fragLib,
  aaIndexIDSet = "all",
  fragLenSet = 3:8,
  fragDepth = 10000,
  fragLibType = c("Deduplicated", "Weighted", "Mock"),
  featureSet = NULL,
  seedSet = 1:5,
  coreN = parallel::detectCores(logical = F),
  tmpDir = file.path(tempdir(), "FeatureDF", format(Sys.time(),
    "%Y.%m.%d.%H.%M.%S"))
)

Arguments

peptideSet	A set of peptide sequences.
fragLenSet	A set of sliding window sizes.
featureSet	A minimum set of features. Combinations of fragment lengths and AAIndex IDs are internally extracted for calculating CPPs.
coreN	The number of cores to be used for parallelization.
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.
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.
seedSet	A set of random seeds.
tmpDir	Destination directory to save intermediate files.

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