SingleCellExperiment-class {SingleCellExperiment} | R Documentation

## The SingleCellExperiment class

### Description

The SingleCellExperiment class is designed to represent single-cell sequencing data. It inherits from the RangedSummarizedExperiment class and is used in the same manner. In addition, the class supports storage of dimensionality reduction results (e.g., PCA, t-SNE) via `reducedDims`, and storage of alternative feature types (e.g., spike-ins) via `altExps`.

### Usage

    SingleCellExperiment(..., reducedDims = list(), altExps = list())

### Arguments

`...` | Arguments passed to the `SummarizedExperiment` constructor to fill the slots of the base class.
`reducedDims` | A list of any number of matrix-like objects containing dimensionality reduction results, each of which should have the same number of rows as the output SingleCellExperiment object.
`altExps` | A list of any number of SummarizedExperiment objects containing alternative Experiments, each of which should have the same number of columns as the output SingleCellExperiment object.

### Details

In this class, rows should represent genomic features (e.g., genes) while columns represent samples generated from single cells. As with any SummarizedExperiment derivative, different quantifications (e.g., counts, CPMs, log-expression) can be stored simultaneously in the `assays` slot, and row and column metadata can be attached using `rowData` and `colData`, respectively.

The `reducedDims` and `altExps` concepts are the main extensions of the SingleCellExperiment class. This enables formalized representation of data structures that are commonly encountered during single-cell data analysis. Readers are referred to the specific documentation pages for more details.

A SingleCellExperiment can also be created by coercing from a SummarizedExperiment or RangedSummarizedExperiment instance.

### Value

A SingleCellExperiment object.

### Author(s)

Aaron Lun and Davide Risso

### See Also

`reducedDims`, for representation of dimensionality reduction results.

`altExps`, for representation of data for alternative feature sets.

`sizeFactors`, to store size factors for normalization.

`?"SCE-combine"`, to combine or subset a SingleCellExperiment object.

`?"SCE-internals"`, for developer use.

### Examples

    ncells <- 100
    u <- matrix(rpois(20000, 5), ncol=ncells)
    v <- log2(u + 1)

    pca <- matrix(runif(ncells*5), ncells)
    tsne <- matrix(rnorm(ncells*2), ncells)

    sce <- SingleCellExperiment(assays=list(counts=u, logcounts=v),
        reducedDims=SimpleList(PCA=pca, tSNE=tsne))
    sce

    ## coercion from SummarizedExperiment
    se <- SummarizedExperiment(assays=list(counts=u, logcounts=v))
    as(se, "SingleCellExperiment")

[Package SingleCellExperiment version 1.9.3 Index]