scater (version 1.0.4)

stand_exprs: Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object.

Description

The stand_exprs element of the arrayData slot in an SCESet object holds a matrix containing standardised (mean-centred, variance standardised, by feature) expression values. It has the same dimensions as the 'exprs' and 'counts' elements, which hold the transformed expression data and count data, respectively.

Usage

stand_exprs(object)
stand_exprs(object) <- value
"stand_exprs"(object)
"stand_exprs"(object)<-value
"stand_exprs"(object)
"stand_exprs"(object) <- value

Arguments

object

a SCESet object.

value

an integer matrix

Value

a matrix of standardised expressiond data

Details

The default for normalised expression values is mean-centred and variance-standardised expression data from the exprs slot of the SCESet object. The function normaliseExprs (or normalizeExprs) provides more options and functionality for normalising expression data.

Examples

data("sc_example_counts")
data("sc_example_cell_info")
example_sceset <- newSCESet(countData = sc_example_counts)
stand_exprs(example_sceset)