bioactivityFingerprint: Create an 'ChemmineR' 'FPset' object that contains...

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

Create an ChemmineR FPset object that contains bioactivity results for a given set of compounds and targets.

Description

Returns a custom binary descriptor fingerprint for a given set of query cids and target compounds, based on the activity data within a bioassaySet object.

Usage

bioactivityFingerprint(bioassaySet, targets = FALSE, summarizeReplicates = "activesFirst")

Arguments

bioassaySet	A bioassaySet object to generate fingeprints from. For a given compound set, this can be generated from a database using the getBioassaySetByCids function.
targets	An optional list of target id(s) to consider when creating the binary fingerprint. If a listed target is not in the bioassaySet, or has no active scores it will still be accepted, but create a fingerprint with all zeros for this location. The binary order of this list is preserved, so that direct comparison and combination of resulting FPset objects created with the same target list can be performed. If omitted, the target list for the bioassaySet object will be used, as returned by the allTargets function.
summarizeReplicates	Optionally allows users to choose how replicates (multiple assays sharing common compounds and targets) are resolved if they disagree. If 'activesFirst' any active score will take precedence over an inactive. If 'mode' the resulting score will be computed according to the statistical mode using as.numeric(names(which.max(table(x)))). Users can also optionally pass a function here which (for each cid/target pair) will receive a list of '2' (active) and '1' (inactive) values, and can then return any desired number as a summary to be included in the resulting table. For a large matrix, the default option 'activesFirst' offers the lowest computational overhead.

Value

The returned object is a standard ChemmineR FPset object, and can be used as described in the ChemmineR documentation. The order and number of binary bits for each compound can be set using the targets option, enabling the combination or comparison of multiple objects created with the same target list. If a single compound has both active and inactive scores for the same target, it will be resolved according to the confictResolver option.

Author(s)

Tyler William H Backman

See Also

Functions: getBioassaySetByCids, getAssays, perTargetMatrix

Examples

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

## retrieve all targets in database
targetList <- allTargets(sampleDB)

## get an activity fingerprint object for selected CIDs
queryCids <- c("2244", "3715", "2662", "3033", "133021", 
    "44563999", "44564000", "44564001", "44564002") 
myAssaySet <- getBioassaySetByCids(sampleDB, queryCids)
myFp <- bioactivityFingerprint(bioassaySet=myAssaySet)

## disconnect from sample database
disconnectBioassayDB(sampleDB)

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