HLA and IPD KIR database for Homo sapiens

Description Usage Arguments Value Slots See Also Examples

This class extends the AnnotationDbi::AnnDbObj-class object by higher level methods for sequence and annotation retrieval. blubb

columns(x)

keytypes(x)

keys(x, keytype, ...)

select(x, keys, columns, keytype, ...)

`x`	the IpdDb object
`keytype`	The keytype for which the keys are retrieved
`...`	Additional arguments. Not used now.
`keys`	The keys for which columns should be selected by select()
`columns`	The columns to retrieve by select

character vector (keys, columns, keytypes) or a data.frame (select).

getDbVersion(): Get the version of the original ipd database
getLoci(): get all loci from a database, see getLoci.
getReference(alleles): Get the reference sequence for alleles, see getReference.
getStructure(alleles): Get the structures of alleles, see getStructure.
getClosestComplete(allele): Get the closest full-length reference sequence of one allele, see getClosestComplete.
getAlleles(locus): Get all alleles of a locus, see getAlleles.

AnnotationDbi::AnnDbObj-class

## load the data 
hla <- loadHlaData()
## get all valid keytypes
kts <- keytypes(hla)
## get all valid columns
cols <- columns(hla)
## get the keys of one keytype
kt <- kts[1]
keys <- keys(hla, kt)
## Get data of the two first columns for the first 10 keys 
cols <- cols[1:10]
res <- select(hla, keys, cols, kt)