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 1.6.0 Index]