The keytypes method for SomaDb objects

keytypes produces a vector of annotation categories that can be used as input keys for the keytype= argument of the select, mapIds, and keys methods. The keytype also informs the query of the format of the search key. For example, when searching the database for annotations corresponding to the gene "NOTCH3", the key "NOTCH3" has the keytype of "SYMBOL". Specifying keytype="SYMBOL" ensures that the gene symbol is not confused for a different identifier ("key") type.

The default keytype ("PROBEID"), corresponds to the SomaLogic SeqId. For more information on database keys, see ?keys.

Usage

# S4 method for SomaDb
keytypes(x)

Arguments

x

the AnnotationDb object. But in practice this will mean an object derived from an AnnotationDb object such as a OrgDb or ChipDb object.

Value

A character vector of all available database keytypes.

Author

Amanda Hiser

Examples

# Retrieve a full list of available keytypes
keytypes(SomaScan.db)
#>  [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT" 
#>  [5] "ENSEMBLTRANS" "ENTREZID"     "ENZYME"       "EVIDENCE"    
#>  [9] "EVIDENCEALL"  "GENENAME"     "GENETYPE"     "GO"          
#> [13] "GOALL"        "IPI"          "MAP"          "OMIM"        
#> [17] "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PFAM"        
#> [21] "PMID"         "PROBEID"      "PROSITE"      "REFSEQ"      
#> [25] "SYMBOL"       "UCSCKG"       "UNIPROT"     

# Specify a keytype other than PROBEID for select
select(SomaScan.db, keys = "NOTCH3", keytype = "SYMBOL",
       columns = "PROBEID")
#> 'select()' returned 1:1 mapping between keys and columns
#>   SYMBOL PROBEID
#> 1 NOTCH3 5108-72