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")
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