SCE-colData: SCE col/rowData methods

Description Usage Arguments Details Value See Also Examples

Description

Methods to obtain column- or row-level metadata from the SingleCellExperiment class.

Usage

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

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

Arguments

x

A SingleCellExperiment object.

...

Further arguments to be passed to the methods for SummarizedExperiment objects, such as use.names.

internal

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

Details

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 event of any name clashes.

Value

colData and rowData return a DataFrame with number of rows equal to ncol(x) and nrow(x), respectively.

See Also

SingleCellExperiment

Examples

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example(SingleCellExperiment, echo=FALSE) # Using the class example
sizeFactors(sce) <- runif(ncol(sce))
isSpike(sce, "ERCC") <- rbinom(nrow(sce), 1, 0.2)==1
rowData(sce, internal=TRUE)
colData(sce, internal=TRUE)

SingleCellExperiment documentation built on May 6, 2019, 4:05 a.m.