allCids {bioassayR} | R Documentation

## List compound cids in a `BioassayDB`, `bioassay`, `bioassaySet`, or target matrix (`dgCMatrix`) object

### Description

Returns a `vector` of small molecule cids contained within a `BioassayDB`, `bioassay`, `bioassaySet`, or target matrix (`dgCMatrix`) object. It can optionally only returned cids labeled as active.

### Usage

    allCids(inputObject, activesOnly = FALSE)

### Arguments

`inputObject` | A `BioassayDB`, `bioassay`, `bioassaySet`, or target matrix (`dgCMatrix`) object to query.
`activesOnly` | logical. Should only active compounds be returned? Defaults to FALSE.

### Value

A `vector` of distinct small molecule cids. No particular order is guranteed.

### 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 all compound cids
    myCids <- allCids(sampleDB)

    ## get only active compound cids
    activeCids <- allCids(sampleDB, activesOnly = TRUE)

    ## disconnect from database
    disconnectBioassayDB(sampleDB)

[Package bioassayR version 1.30.0 Index]