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DESCRIPTION 100644 1 kb
NAMESPACE 100644 1 kb 100644 2 kb
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. ```r 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") ```