normalizeData: Normalize Datasets

In nbenn/singleCellFeatures: Analyze single cell features stored in an openBIS instance

Description

After running aggregate, bscore or MARS augmentation functions, this function can be used for centering and scaling data.

Usage

normalizeData(x, ...)

Arguments

x	The Data object of interest.
select	A vector of regular expressions for selecting features to normalize.
drop	A vector of regular expressions for dropping some of the previously matched features.
values	The type of features to normalize.
center	NULL of the type of features to use for centering.
scale	NULL of the type of features to use for scaling
features	For internal use only.

Value

A Data object of input type with normalized features added.

Examples

data <- PlateData(PlateLocation("J101-2C"))
data <- augmentImageLocation(data)
data <- augmentCordinateFeatures(data, ellipse=1, facet=NULL,
                                 center.dist=FALSE, density=FALSE)
data <- augmentBscore(data)
data <- augmentMars(data)

data <- augmentAggregate(data, features="_MARSed$", level="plate",
                         func.aggr="median")
data <- augmentAggregate(data, features="_MARSed$", level="well",
                         neighbors=TRUE,  func.aggr="mad")
data <- normalizeData(data)

nbenn/singleCellFeatures documentation built on May 23, 2019, 12:24 p.m.