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 allows storage of multiple vectors of size factors (e.g., different values for spike-ins versus endogenous genes). If type is NULL, a “default” set of size factors is stored or returned.

If value is NULL for isSpike<-, size factors of type will be removed from object. All size factors can be removed from object by using the clearSizeFactors method.

The sizeFactorNames method will return the names of all stored size factor sets. This does not include the default set of size factors (obtained with isSpike(..., type=NULL)) as these are unnamed.

Value

For sizeFactors, a numeric vector is returned containing size factors of the set type for all cells. If type is not available, NULL is returned instead.

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)

sizeFactors(sce, "ERCC") <- runif(ncol(sce)) 
sizeFactors(sce, "ERCC")
sizeFactors(sce) # unchanged.

sizeFactors(sce, "ERCC") <- NULL
sizeFactors(sce, "ERCC") 

[Package SingleCellExperiment version 1.4.1 Index]