queryBioassayDB: Perform a SQL query on a bioassayR database

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

Perform a SQL query on a bioassayR database

Description

Provides extreme query flexibility by allowing the user to perform any SQLite query on a bioassayR database. This allows for analysis beyond that provided by the built in query functions.

Usage

queryBioassayDB(object, query)

Arguments

object	A BioassayDB object referring to a bioassayR database.
query	A string containing a valid SQLite query (see SQLite documentation for more details).

Value

A data.frame containing the results of the specified query.

Author(s)

Tyler Backman

References

http://www.sqlite.org provides a complete reference for SQLite syntax that can be used with this function

Examples

## connect to a test database
extdata_dir <- system.file("extdata", package="bioassayR")
sampleDatabasePath <- file.path(extdata_dir, "sampleDatabase.sqlite")
sampleDB <- connectBioassayDB(sampleDatabasePath)

## inspect the structure of the database before forming a query
queryBioassayDB(sampleDB, "SELECT * FROM sqlite_master WHERE type='table'")

## find all activity data for compound cid 2244 
queryBioassayDB(sampleDB, "SELECT * FROM activity WHERE cid = '2244'")

## disconnect from database
disconnectBioassayDB(sampleDB)

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