| Title: | IPD IMGT/HLA and IPD KIR database for Homo sapiens |
|---|---|
| Description: | All alleles from the IPD IMGT/HLA <https://www.ebi.ac.uk/ipd/imgt/hla/> and IPD KIR <https://www.ebi.ac.uk/ipd/kir/> database for Homo sapiens. 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. |
| Authors: | Steffen Klasberg |
| Maintainer: | Steffen Klasberg <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.25.0 |
| Built: | 2024-11-29 08:12:13 UTC |
| Source: | https://github.com/bioc/ipdDb |
Get all alleles of a given locus.
getAlleles(x, locus)getAlleles(x, locus)
x |
The database connection; an |
locus |
A single locus as a string. |
A character vector with all alleles of the give locus.
## Load the database hla <- loadHlaData() ## Get the loci loci <- getLoci(hla) ## Get alleles of a locus alleles <- getAlleles(hla, loci[1])## Load the database hla <- loadHlaData() ## Get the loci loci <- getLoci(hla) ## Get alleles of a locus alleles <- getAlleles(hla, loci[1])
Get the sequence of the closest allele which for which a full-length sequence is available.
getClosestComplete(x, allele, locus = NULL)getClosestComplete(x, allele, locus = NULL)
x |
The database connection; an |
allele |
A single allele as a string. |
locus |
optional parameter used if the allele identifier is not found. |
A Biostrings:DNAStringSet
object with the sequence
of the closest full-length allele.
## Load the database hla <- loadHlaData() ## Get the loci loci <- getLoci(hla) ## Get alleles of a locus alleles <- getAlleles(hla, loci[1]) alleleOfInterest <- alleles[1] ## Get the closest complete sequence seqs <- getClosestComplete(hla, alleleOfInterest, loci[1])## Load the database hla <- loadHlaData() ## Get the loci loci <- getLoci(hla) ## Get alleles of a locus alleles <- getAlleles(hla, loci[1]) alleleOfInterest <- alleles[1] ## Get the closest complete sequence seqs <- getClosestComplete(hla, alleleOfInterest, loci[1])
Get all available loci of the KIR or HLA database
getLoci(x)getLoci(x)
x |
The database connection; an |
A vector of available loci in the database.
## Load the database hla <- loadHlaData() ## Get the loci loci <- getLoci(hla)## Load the database hla <- loadHlaData() ## Get the loci loci <- getLoci(hla)
Get the reference sequences for alleles.
getReference(x, allele)getReference(x, allele)
x |
The database connection; an |
allele |
The alleles of interest as a character vector. |
A Biostrings:DNAStringSet
object with all references.
## Load the database hla <- loadHlaData() ## Get the loci loci <- getLoci(hla) ## Get alleles of a locus alleles <- getAlleles(hla, loci[1]) allelesOfInterest <- alleles[1:10] ## Get the sequences seqs <- getReference(hla, allelesOfInterest)## Load the database hla <- loadHlaData() ## Get the loci loci <- getLoci(hla) ## Get alleles of a locus alleles <- getAlleles(hla, loci[1]) allelesOfInterest <- alleles[1:10] ## Get the sequences seqs <- getReference(hla, allelesOfInterest)
Get the gene structures for alleles.
getStructure(x, allele)getStructure(x, allele)
x |
The database connection; an |
allele |
The alleles of interest as a character vector. |
A GenomicRanges:GRanges
object with all gene
structures.
## Load the database hla <- loadHlaData() ## Get the loci loci <- getLoci(hla) ## Get alleles of a locus alleles <- getAlleles(hla, loci[1]) allelesOfInterest <- alleles[1:10] ## Get the structures seqs <- getStructure(hla, allelesOfInterest)## Load the database hla <- loadHlaData() ## Get the loci loci <- getLoci(hla) ## Get alleles of a locus alleles <- getAlleles(hla, loci[1]) allelesOfInterest <- alleles[1:10] ## Get the structures seqs <- getStructure(hla, allelesOfInterest)
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, ...)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)## 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)
This package holds the IPD IMGT/HLA and IPD KIR database. All alleles are accessible using the select, columns, keys and keytypes methods of the AnnoatationDbi package of bioconductor.
Included data are:
Allele names
p-groups
g-groups
cwd_status
completeness status
gene structure
reference sequences
closest full-length allele
Load the IPD IMGT/HLA database
loadHlaData(version = "Latest")loadHlaData(version = "Latest")
version |
Either a valid version of the IPD IMGT/HLA database or "Latest" to fetch the latest version |
an IpdDb object containing the database.
## Load the HLA database hla <- loadHlaData()## Load the HLA database hla <- loadHlaData()
Load the IPD KIR database
loadKirData(version = "Latest")loadKirData(version = "Latest")
version |
Either a valid version of the IPD KIR database or "Latest" to fetch the latest version |
an IpdDb object containing the database.
## Load the KIR database kir <- loadKirData()## Load the KIR database kir <- loadKirData()