binders: Find MHC Binders in Protein Sequence

In EpitopePrediction: Predict Binding Between Peptides and MHC Molecules

Description

Performs binding predictions for all l-mers in the given protein sequence, extracts the peptide whose IC50 values are below the given thresholds, and returns the results as a data frame.

Usage

binders(x, mhc = "HLA-A-02:01", l = 9, ic50.threshold = 500,
  quantile.threshold = NULL, include.peptide = TRUE, method = "smm")

Arguments

x	string, a protein sequence given in single-letter coding. Only the 20 common amino acids are supported.
mhc	string identifying the MHC molecule.
l	the peptide length.
ic50.threshold	peptides with a predicted IC50 value lower than this will be considered binders. A threshold of 500 nM is common. Use Inf to show predictions for all peptides of length l.
quantile.threshold	a number between 0 and 1. If this is not NULL, then the parameter ic50.threshold is ignored and the peptides for which the predicted IC50 falls within the given quantile will be returned. For instance, a value of .02 return the peptides whose binding strength is in the top 2% for the given protein.
include.peptide	logical, whether to include the actual peptide in the output data frame. This may not be desired in some circumstances, e.g. for very long proteins or for converting the result to a matrix.
method	string defining which prediction method to use. Currently the only implemented method is the stabilized matrix method (SMM), such that this setting is ignored. But further methods may be implemented in the future.

Value

a data frame containing the peptide (if include.peptide=TRUE), start position, end position, and predicted IC50 for every peptide below the threshold.

Examples

## This is the CORE protein from the Hepatitis C virus reference sequence available
## at https://hcv.lanl.gov/content/sequence/LOCATE/locate.html
hcv.core <- paste("MSTNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRR",
"QPIPKARRPEGRTWAQPGYPWPLYGNEGCGWAGWLLSPRGSRPSWGPTDPRRRSRNLGKVIDTLTCGFADLMGYIPLVGA",
 "PLGGAARALAHGVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPASA",sep="")
binders( hcv.core )

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