Functions re-exported from other packages

These are some commonly used getters and setters of classes that SFE inherits so you don't have to separately attach those packages to use these functions.

Usage

colData(x, ...)

rowData(x, use.names = TRUE, ...)

colData(x, ...) <- value

spatialCoords(x, ...)

spatialCoords(x) <- value

spatialCoordsNames(x)

getImg(x, ...)

imgData(x)

rmvImg(x, ...)

counts(object, ...)

logcounts(object, ...)

reducedDim(x, type, ...)

Arguments

x

A SummarizedExperiment object.

...

For assay, arguments in ... are forwarded to assays.

For rbind, cbind, ... contains SummarizedExperiment objects to be combined.

For other accessors, ignored.

use.names

For rowData: Like mcols(x), by default rowData(x) propagates the rownames of x to the returned DataFrame object (note that for a SummarizedExperiment object, the rownames are also the names i.e. rownames(x) is always the same as names(x)). Setting use.names=FALSE suppresses this propagation i.e. it returns a DataFrame object with no rownames. Use this when rowData(x) fails, which can happen when the rownames contain NAs (because the rownames of a SummarizedExperiment object can contain NAs, but the rownames of a DataFrame object cannot).

For combineRows and combineCols: See Combining section below.

value

An object of a class specified in the S4 method signature or as outlined in ‘Details’.

object

A SingleCellExperiment object, which includes SFE.

type

Name or numeric index to indicate which reducedDim to get, such as "PCA". By default the first item in reducedDims.