Miscellaneous SCE {SingleCellExperiment}R Documentation

Miscellaneous SCE methods

Description

Various methods for the SingleCellExperiment class.

Usage

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

## S4 method for signature 'SingleCellExperiment'
objectVersion(x)

## S4 method for signature 'SingleCellExperiment'
colData(x, internal=FALSE)

## S4 method for signature 'SingleCellExperiment'
rowData(x, internal=FALSE)

Arguments

x, object

A SingleCellExperiment object.

internal

Whether the information contained in the internal slots should be returned.

Details

The show method will print out information about the data contained in object. This describes the stored assays and row/column metadata, as done in show,SummarizedExperiment-method. The names of the reducedDims slot and the names of the spike-ins (see spikeNames) are also reported.

The objectVersion method will return the version of the package with which x was constructed. This is useful for checking if the object is up to date relative to the latest versions of the package.

It may sometimes be useful to return both the visible and the internal colData in a single DataFrame (see SingleCellExperiment-class). This can be achieved by using colData(x, internal=TRUE), which will return the stored colData along with the int_colData (currently the sizeFactors). Similarly, rowData(x, internal=TRUE) will return the stored rowData along with the int_rowData (currently the columns corresponding to isSpike). Warnings will be raised in the unlikely event of any name clashes.

Value

For show, a message is printed to screen describing the data stored in object.

For objectVersion, an object of class package_version is returned.

colData and rowData return a DataFrame.

See Also

spikeNames

Examples

example(SingleCellExperiment, echo=FALSE) # Using the class example
show(sce)
objectVersion(sce)

sizeFactors(sce) <- runif(ncol(sce))
isSpike(sce, "ERCC") <- rbinom(nrow(sce), 1, 0.2)==1
rowData(sce, internal=TRUE)
colData(sce, internal=TRUE)

[Package SingleCellExperiment version 1.2.0 Index]