loadIdMapping: Load a target identifier mapping into a bioassayR database

Description Usage Arguments Author(s) References See Also Examples

View source: R/loadingData.R

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

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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

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## 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)

bioassayR documentation built on March 1, 2021, 2 a.m.