ipdDb

Database package of HLA and KIR alleles from the IPD IMGT/HLA | Github and IPD KIR | Github databases.

Reference:

Robinson J, Maccari G, Marsh SGE, Walter L, Blokhuis J, Bimber B, Parham P, De Groot NG, Bontrop RE, Guethlein LA, and Hammond JA
KIR Nomenclature in non-human species
Immunogenetics (2018), in preparation

This package holds all information from the IPD databases. For HLA this is limited to HLA-A, -B, -C, -DPB1, -DQB1 and -DRB1.

For alleles which are not known in full-length, also the closest full-length allele is stored.

The data is stored in an SQLite database and its compatible with Bioconductor’s database package rules, i.e. the select method including columns, keytypes and keys.

Additionally, some helper functions are implemented to fetch all contained loci, all alleles of a locus, the sequences of alleles and the sequence of closest allele which is available in full-length for an allele.

library(ipdDb)

hla <- loadHlaData()
## get all loci stored in the db
available_loci <- hla$getLoci()

## get all alleles of a locus
alleles <- hla$getAlleles(available_loci[1])
alleles <- hla$getAlleles("HLA-A")

## get all sequences of a bunch of alleles as DNAStringSet
sequences <- hla$getReference(alleles)
sequences <- hla$getReference(c("HLA-A*01:01:01:01", "HLA-A*01:01:01:03" ))

## get the closest complete reference for ONE allele as DNAStringSet
closest_complete <- hla$getClosestComplete(alleles[1])
closest_complete <- hla$getClosestComplete("HLA-A*01:01:01:01")

## Get the gene structure for a bunch of alleles as GRanges object
structures <- hla$getStructure(alleles)
structures <- hla$getStructure(c("HLA-A*01:01:01:01", "HLA-A*01:01:01:03" ))

## specifiy the database version
hla <- loadHlaData(version = "3.32.0")