stand_exprs: Accessors for the 'stand_exprs' (standardised expression)...

In dynverse/scaterlegacy: Single-cell analysis toolkit for gene expression data in R

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

## S4 method for signature 'SCESet'
stand_exprs(object)

## S4 replacement method for signature 'SCESet,matrix'
stand_exprs(object)<-value

## S4 method for signature 'SCESet'
stand_exprs(object)

## S4 replacement method for signature 'SCESet,matrix'
stand_exprs(object) <- value

Arguments

object	a SCESet object.
value	an integer matrix

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.

Value

a matrix of standardised expressiond data

Author(s)

Davis McCarthy

Examples

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

dynverse/scaterlegacy documentation built on Feb. 17, 2020, 5:07 a.m.