selectiveAgainst: Identify small molecules with selective binding against a...

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

Identify small molecules with selective binding against a target of interest

Description

Allows the user to find compounds in the database that have been screened against a large number of distinct targets, but show high binding selectivity for a specific target of interest.

Usage

selectiveAgainst(database, target, maxCompounds = 10, minimumTargets = 10)

Arguments

database	A BioassayDB database to query.
target	A string or integer containing a target_id referring to a target of interest.
maxCompounds	An integer representing the number of resulting compounds to return.
minimumTargets	An integer representing the minimum number of distinct targets a compound must have been screened against to be included in the results.

Value

A data.frame where the row names represent each compound showing binding specificity against the specified target. The first column shows the number of distinct targets each compound shows activity against, and the second column shows the total number of distinct targets it has been screened against.

Author(s)

Tyler Backman

Examples

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

## find target selective compounds active against a protein of interest
selectiveAgainst(sampleDB, target="166897622", maxCompounds=10,minimumTargets=20)

## disconnect from database
disconnectBioassayDB(sampleDB)

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