translateTargetId: Translate a protein target identifier to another identifier...

In girke-lab/bioassayR: Cross-target analysis of small molecule bioactivity

Translate a protein target identifier to another identifier system

Description

Returns a character vector of the protein target identifiers using the specified category (classification system). This is most often used to translate NCBI Protein GI numbers (as provided with the pre-build PubChem Bioassay database) into UniProt identifiers.

Usage

translateTargetId(database, target, category, fromCategory = "GI")

Arguments

database	A BioassayDB database to query.
target	A protein target identifier to query (as set by the category option, with a default of "GI").
category	The specified identifier type to return, such as 'UniProt'.
fromCategory	The identifier type of the query (default "GI").

Value

A character vector of the protein target identifiers of the category specified for the target specified. An NA is returned if no matching values exist in the database.

Author(s)

Tyler Backman

References

http://www.ncbi.nlm.nih.gov/protein NCBI Protein Database http://www.uniprot.org UniProt Protein Database

See Also

loadIdMapping

Examples

## create sample database
myDatabaseFilename <- tempfile()
mydb <- newBioassayDB(myDatabaseFilename, indexed=FALSE)

## load a sample translation from GI 6686268 to UniProt P11712
loadIdMapping(mydb, "6686268", "UniProt", "P11712")

## get UniProt identifier(s) for GI Number 6686268
UniProtIds <- translateTargetId(mydb, "6686268", "UniProt")
UniProtIds

## get GI identifier(s) for UniProt ID P11712
GIs <- translateTargetId(mydb, "P11712", "GI", "UniProt")
GIs

## disconnect from and delete sample database
disconnectBioassayDB(mydb)
unlink(myDatabaseFilename)

girke-lab/bioassayR documentation built on Oct. 22, 2024, 8:13 a.m.