Size factor methods {SingleCellExperiment}R Documentation

Size factors methods

Description

Gets or sets the size factors for all cells.

Usage

## S4 method for signature 'SingleCellExperiment'
sizeFactors(object, type=NULL)

## S4 replacement method for signature 'SingleCellExperiment'
sizeFactors(object, type=NULL) <- value

## S4 method for signature 'SingleCellExperiment'
clearSizeFactors(object)

## S4 method for signature 'SingleCellExperiment'
sizeFactorNames(object)

Arguments

object

A SingleCellExperiment object.

type

A string specifying the type of size factor to get or set.

value

A numeric vector of size factors for all cells.

Details

A size factor is a scaling factor used to divide the raw counts of a particular cell to obtain normalized expression values. The sizeFactors methods can be used to get or set size factors for all cells.

The type argument is deprecated, as are the sizeFactorNames and clearSizeFactors functions.

Value

For sizeFactors, a numeric vector is returned containing size factors for all cells.

For sizeFactors<-, a SingleCellExperiment is returned with size factors stored in the internal metadata fields.

For clearSizeFactors, a SingleCellExperiment is returned with no size factor information.

For sizeFactorNames, a character vector is returned containing the names of all named size factor sets.

Author(s)

Aaron Lun

See Also

SingleCellExperiment-class

Examples

example(SingleCellExperiment, echo=FALSE) # Using the class example
sizeFactors(sce) <- runif(ncol(sce))
sizeFactors(sce)

[Package SingleCellExperiment version 1.8.0 Index]