Package index • deepMatchR

HLA Genotypes

Create and work with HLA genotype objects

hlaGeno(): Create an hla_genotype object
validateHlaGeno(): Validate an hla_genotype object
print(<hla_genotype>): Print an hla_genotype object

Sequence Analysis

Functions for retrieving and comparing HLA sequences

getAlleleSequence(): Get Sequence for an HLA Allele
quantifyMismatch(): Quantify Amino Acid Mismatches With Charge/Polarity Awareness (base R)
calculateMismatchLoad(): Calculate Mismatch Load Between Donor and Recipient Genotypes
getSequenceStats(): Get Sequence Statistics
clearSequenceCache(): Clear Sequence Cache

Eplet Analysis

Functions for eplet-based immunogenicity analysis

quantifyEpletMismatch(): Quantify Eplet Mismatches Between Two Alleles
calculateEpletLoad(): Calculate Eplet Load Between Donor and Recipient Genotypes

Peptide Binding Prediction

Deep learning models for peptide-MHC binding prediction

predictMHCnuggets(): Predict peptide–MHC binding with mhcnuggets
calculatePeptideBindingLoad(): Calculate Peptide Binding Load for Transplant Risk Assessment
visualizePeptideBinding(): Visualize Cross-Locus Peptide Binding Results

Serology Conversion

Convert between molecular and serological HLA nomenclature

toSerology(): Convert HLA Alleles to Serological Equivalents
updateWmdaData(): Update WMDA Nomenclature Data
clearWmdaCache(): Clear WMDA Cache

Antibody Visualization

Visualize SAB and PRA assay results

plotAntibodies() plotSAB() plotPRA(): Plot Antibody Data with Optional Antigen-Level Table or Time-Series Trend
plotEplets(): Plot Eplet Results from SPI Assay
calculateAUC() epletAUC() cregAUC() serologyAUC(): Calculate Antigen AUC Based on MFI

Data

Built-in datasets

deepMatchR_example: Example SAB (Class I/II) and PRA Panels
deepMatchR_cregs: CREG–Allele Mapping Data
deepMatchR_eplets: HLA Eplet Assignments (Registry-derived)
deepMatchR_wmda_pgroups: WMDA P-Group Definitions
deepMatchR_wmda_serology: WMDA DNA-to-Serology Mapping
deepMatchR_wmda_splits: WMDA Broad-to-Split Antigen Relationships

Utilities

Helper functions and internal utilities

deepmatchrEnv(): Return a Basilisk environment tailored to the current platform
batchGetSequences(): Batch Get Sequences with Parallel Processing