screenedAtLeast {bioassayR} | R Documentation

## Return all compounds in the database screened at least 'minTargets' times.

### Description

Returns all compound cids screened against at least 'minTargets' distinct target identifiers. For a very large database (such as PubChem Bioassay) this function may take a long time to run.

### Usage

    screenedAtLeast(database, minTargets, inconclusives=TRUE)

### Arguments

`database` | A `BioassayDB` database to query.
`minTargets` | The minimum number of distinct targets for each returned cid.
`inconclusives` | Logical. If `TRUE` (the default) screening results with inconclusive (`NA`) are counted towards `minTargets`. If `FALSE` only active and inactive results are counted.

### Value

Returns a `character` vector of all CIDs meeting the specified criteria.

### 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 CIDS screened against at least 2 distinct targets
    highlyScreened <- screenedAtLeast(sampleDB, 2)
    highlyScreened

    ## get all CIDS screened against at least 2 distinct targets with conclusive results
    highlyScreened <- screenedAtLeast(sampleDB, 2, inconclusives=FALSE)
    highlyScreened

    ## disconnect from database
    disconnectBioassayDB(sampleDB)

[Package bioassayR version 1.32.1 Index]