getBioassaySetByCids: Create 'bioassaySet' sparse matrix object with activity data...

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

Create bioassaySet sparse matrix object with activity data only for specified compounds

Description

Takes a list of compounds, and creates a bioassaySet sparse matrix object with the activity data for these compounds only, not including activity data from other compounds in the same assays.

Usage

getBioassaySetByCids(database, cids)

Arguments

database	A BioassayDB database to query.
cids	One or more compounds IDs of interest.

Value

A bioassaySet object containing data from the specified cids.

Author(s)

Tyler William H Backman

Examples

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

## retrieve activity data on 3 compounds 
activitySet <- getBioassaySetByCids(sampleDB, c("2244","3715","237"))
activitySet

## disconnect from sample database
disconnectBioassayDB(sampleDB)

girke-lab/bioassayR documentation built on April 28, 2022, 7:34 a.m.