mhcI: Prediction of Nonself Peptide Presentation on Human MHC Class...

In epitopeR: Predict Peptide-MHC Binding

Prediction of Nonself Peptide Presentation on Human MHC Class I

Description

It determines which non-self peptides can be presented by a given HLA class I allele. This function takes a sequence for a stimulating antigen and the corresponding self antigen, and given a defined sequence length, queries the IEDB API with the user's choice of peptide binding prediction method. The set of peptides present in the results for the stimulating antigen but not the self antigen are then carried forward as non-self peptides. If desired, the user can adjust the default thresholds (by IC50 binding affinity or percentile rank) used to define "strong" and "weak" binders. The output is a dataframe of non-self peptides that are predicted to bind to the presenting allele.

Usage

mhcI(
  ag_present,
  ag_stim,
  ag_self = "",
  seq_len = "9",
  fd_out = as.character(paste0(tempdir(), "/", "outputs", "/")),
  method = "consensus",
  thold_ic50 = c(50, 500),
  thold_pect_rank = c(2, 10),
  url_iedb = "http://tools-cluster-interface.iedb.org/tools_api/mhci/",
  noneself = TRUE
)

Arguments

ag_present	character vector, presenting allele, formatting examples - A*01:01 or HLA-A*01:01
ag_stim	character vector, stimulating antigen, can either be an HLA class I allele entered in the same format as ag_present, or a character vector of the amino acid sequence of the protein
ag_self	character, self antigen, can either be an HLA class I allele entered in the same format as ag_present, or a character vector of the amino acid sequence of the protein
seq_len	string, length of peptides to consider
fd_out	string, output folder name, set to tempdir()
method	string, IEDB prediction method to be used. Options are ann, comblib_sidney2008, consensus, netmhccons, netmhcpan, netmhcpan_ba netmhcpan_el, netmhcstabpan, pickpocket, recommended, smm, smmpmbec. Default is netmhcstabpan
thold_ic50	vector. Defines the thresholds required to be included in results, and to be labeled, "strong" or "weak" binder. Multiple prediction methods are used, each of which provide different raw outputs (i.e. IC50, "strength", "score"). Our justification for the default thresholds is listed in the mhcI_hu vignette, however the user may choose to specify alternate cutoffs if desired.
thold_pect_rank	vector, IEDB adjusts all outputs in comparison to a set of random natural peptides in order to determine an normalized adjusted percentile rank. With normalized ranks, the same thresholds can be used across different methods. Default thresholds are <2% for strong binders and <10% for weak binders.
url_iedb	string, iedb api url
noneself	logic, whether to subtract self peptide from stim. If TRUE|T, self peptides will be subtracted from stim. If FALSE|F no self subtraction.

Value

data frame, MHC I binding prediction result table

Examples

mhcI(ag_present=c("HLA-A*03:01"),
ag_stim=c("A_01_01","A_02_06"),
ag_self=c("B_07_03"),
method = "rec")

epitopeR documentation built on Feb. 16, 2023, 7:06 p.m.