activeAgainst: Show compounds active against a specified target

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

Show compounds active against a specified target

Description

Returns a data.frame of small molecule cids which show activity against a specified target. Each row name represents a cid which shows activity, and the total screens and the percent active are shown in their respective columns.

Usage

activeAgainst(database, target)

Arguments

database	A BioassayDB database to query.
target	A string or integer containing a target_id referring to a target of interest.

Value

A data.frame where the row names represent each compound showing activity against the specified target. The second column shows the number of distinct assays in which this cid was screened against the target, and the first column shows the percentage of these which exhibited activity.

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)

## get cids of compounds which show activity against target 116516899
myCids <- row.names(activeAgainst(sampleDB, "166897622"))

## disconnect from database
disconnectBioassayDB(sampleDB)

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