loadIdMapping: Load a target identifier mapping into a bioassayR database

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

Load a target identifier mapping into a bioassayR database

Description

Loads an identifier mapping for a bioassay target (stored in the database as an NCBI GI number) to another protein target naming system. Common uses include UniProt identifiers, similarity clusters, and common names.

Usage

loadIdMapping(database, target, category, identifier)

Arguments

database	A writable BioassayDB database to insert data into.
target	A single protein target NCBI GI number.
category	The specified identifier type of the data being loaded, such as 'UniProt'.
identifier	A character object with the new identifier. This should be length one, and the function should be re-ran to add multiple identifiers.

Author(s)

Tyler Backman

References

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

See Also

translateTargetId

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

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

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