sizeFactors {SingleCellExperiment} | R Documentation

## Size factor methods

### Description

Gets or sets the size factors for all cells in a SingleCellExperiment object.

### Usage

    ## S4 method for signature 'SingleCellExperiment'
    sizeFactors(object, onAbsence = "none")

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

### Arguments

`object` | A SingleCellExperiment object.
`onAbsence` | String indicating an additional action to take when size factors are absent: nothing (`"none"`), a warning (`"warn"`) or an error (`"error"`).
`...` | Additional arguments, currently ignored.
`value` | A numeric vector of length equal to `ncol(object)`, containing 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, thus allowing downstream comparisons between cells that are not affected by differences in library size or total RNA content. The `sizeFactors` methods can be used to get or set size factors for all cells in a SingleCellExperiment object.

When setting size factors, the values are stored in the `colData` as the `sizeFactors` field. This name is chosen for general consistency with other packages (e.g., DESeq2) and to allow the size factors to be easily extracted from the `colData` for use as covariates.

For developers, `onAbsence` is provided to make it easier to mandate that `object` has size factors. This avoids silent `NULL` values that flow to the rest of the function and make debugging difficult.

### Value

For `sizeFactors`, a numeric vector is returned containing size factors for all cells. If no size factors are available, a `NULL` is returned (and/or a warning or error, depending on `onAbsence`).

For `sizeFactors<-`, a modified `object` is returned with size factors in its `colData`.

### Author(s)

Aaron Lun

### See Also

SingleCellExperiment, for the underlying class definition.

`librarySizeFactors` from the scater package or `computeSumFactors` from the scran package, as examples of functions that compute the size factors.

### Examples

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

[Package SingleCellExperiment version 1.9.3 Index]