cross_background: Creating immunopeptidomics database

In oandrefonseca/crossdome: An R package to measure cross-reactivity risk in the sequence-space

Creating immunopeptidomics database

Description

Peptide database spanning eluted candidates (experimentally validated) and custom (user-defined).

Usage

cross_background(off_targets = NULL, allele)

Arguments

off_targets	A list of off-target candidates. Only 9-mers are supported.
allele	Input an MHC Class I allele. Please, check hla_database.

Value

Returns a xrBackground object

Examples

## Not run: 

# Listing MHC class I alleles
data('hla_database')
View(hla_database)

# Using default immunopeptidomics
background <- cross_background(allele = 'HLA-A*01:01')

# Using MAGE3A off-targets
data('mage_off_targets')

mage_off_targets <- mage_off_targets$peptide_sequence
background <- cross_background(off_targets = mage_off_targets, allele = "HLA-A*01:01")


## End(Not run)

oandrefonseca/crossdome documentation built on March 30, 2023, 7:10 p.m.