scaleBioassaySet: Centers and standardizes the numeric activity scores for a...

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

Centers and standardizes the numeric activity scores for a bioassaySet object (creates Z-scores)

Description

Converts the numeric activity scores for a bioassaySet object into per-assay Z-scores. Untested '0' values are not considered in computing the value, only actives and inactives. In essence, this is a special version of the R base scale function, which ignores missing entries in a sparse matrix instead of using them as zeros. A primary purpose of this function is to pass scaled results to perTargetMatrix, in order to compute a numeric Z-score compound vs. target matrix.

Usage

scaleBioassaySet(bioassaySet, center=TRUE, scale=TRUE)

Arguments

bioassaySet	A bioassaySet object with data from multiple assays. This should be created with getAssays rather than getBioassaySetByCids, as the former includes the full assay data whereas the latter omits scores for compounds other than those specified, and therefore will not compute a coherent Z-score.
center	A logical value. If center is TRUE then centering is done by subtracting the assay means (omitting inconclusive NAs) from their corresponding scores, and if center is FALSE, no centering is done.
scale	A logical value. Scaling is done by dividing the (centered) per-assay scores by their standard deviations if center is TRUE, and the root mean square otherwise. If scale is FALSE, no scaling is done.

Value

A bioassaySet object with standardized numeric scores, that can be accessed with scores(bioassaySet).

Author(s)

Tyler William H Backman

See Also

Functions: 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 three assays
assays <- getAssays(sampleDB, c("347221","53211","624349"))

## disconnect from sample database
disconnectBioassayDB(sampleDB)

## compute and return standardized scores
scaledAssays <- scaleBioassaySet(assays)

## inspect scaled and unscaled scores
scores(assays)
scores(scaledAssays)

## NOTE: this example only returns non-NA Z-scores if tried with
## real data, not the test database used here

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