smm: Peptide-MHC Binding Prediction

In EpitopePrediction: Predict Binding Between Peptides and MHC Molecules

Description

Predicts peptide-MHC binding using the stabilized matrix method (SMM) algorithm with a specifically constructed amino acid substitution matrix. See citation(package='EpitopePrediction') for the reference.

Usage

smm(x = c("SLYNTVATL", "SYFPEITHI"), mhc = "HLA-A-02:01",
  output.IC50 = TRUE)

Arguments

x	vector of strings containing the peptides for which to predict MHC binding.
mhc	string or vector of strings identifying the MHC molecules. See supportedMHCs for allowed values. If a vector is given, it must be of the same length as x.
output.IC50	whether to output the IC50 value itself (default) or its base10-logarithm.

Examples

## Predict IC50 binding values for two famous peptides
smm( c("SLYNTVATL","SYFPEITHI"), "HLA-A-02:01" )

EpitopePrediction documentation built on May 2, 2019, 6:18 p.m.