IpdDb-class {ipdDb} | R Documentation |
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
.
## 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)