SingleTCRAnalysis: Single TCR-peptide contact potential profiling.

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

Single TCR-peptide contact potential profiling.

Description

Single TCR-peptide contact potential profiling.

Usage

contactFootprintDensityPlot(weightStringSet)

Features_sCPP(
  peptideSet,
  tcrSet,
  aaIndexIDSet = c("BETM990101inv", "KESO980102inv", "KOLA930101", "MICC010101",
    "SIMK990104", "VENM980101", "VENM980101inv"),
  fragLenSet = 3:8,
  seed = 12345,
  coreN = parallel::detectCores(logical = F)
)

univariateCorrelationAnalysis(
  dt_deltaG_sCPP,
  coreN = parallel::detectCores(logical = F)
)

univariateCorrelationPlot(
  dt_deltaG_sCPP,
  dt_deltaG_sCPP_outlier = NULL,
  corVarName = "sCPP_BETM990101inv_Skew_4"
)

univariateFeatureSelect(dt_univ, aaIndexIDSet, sig = 0.05, bestOnly = T)

multivariateRegressionPlot(
  dt_deltaG_sCPP,
  dt_deltaG_sCPP_outlier = NULL,
  corVarNames
)

multivariateRegressionPrediction(
  dt_deltaG_sCPP,
  dt_deltaG_sCPP_new = NULL,
  corVarNames
)

Arguments

weightStringSet	A set of contact weights. E.g. "1|2|3|2|1"
peptideSet	A set of peptide sequences.
tcrSet	A set of corresponding TCR sequences.
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. Must be between 3 and 8.
seed	A random seed.
coreN	The number of cores to be used for parallelization.
dt_deltaG_sCPP	A data.table containing the "DeltaG" and sCPP feature columns.
dt_deltaG_sCPP_outlier	Optional. If provided, it would be used as outliers.
corVarName	A variable name used for univariate analysis.
dt_univ	An output data.table of univariate analysis.
sig	A siginificance cutoff for univariate feature selection.
bestOnly	Logical. If True, only the best sCPP feature per AAIndex will be returned. If False, all sCPP features derived from selected AAIndices will be returned.
corVarNames	A set of variable names used for multivariate regression.
dt_deltaG_sCPP_new	Optional. If provided, TCR affnities would be predicted for this dataset. Otherwise, predicted TCR affinities for the original dataset would be returned.

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