R: Reduced dimensions methods

Reduced dimensions {SingleCellExperiment}

R Documentation

Reduced dimensions methods

Description

Methods to get or set the dimensionality reduction results.

Usage

## S4 method for signature 'SingleCellExperiment'
reducedDim(x, type=1, withDimnames=TRUE)

## S4 replacement method for signature 'SingleCellExperiment'
reducedDim(x, type=1) <- value

## S4 method for signature 'SingleCellExperiment'
reducedDims(x, withDimnames=TRUE)

## S4 replacement method for signature 'SingleCellExperiment'
reducedDims(x) <- value

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

## S4 replacement method for signature 'SingleCellExperiment,character'
reducedDimNames(x) <- value

Arguments

`x`	A SingleCellExperiment object.
`type`	A string containing the name for the dimensionality reduction results or a numeric index containing the position of the desired dimenionality reduction result.
`withDimnames`	A logical scalar indicating whether each set of results should be returned with row names matching `colnames(x)`. This can be turned off for greater efficiency.
`value`	For `reducedDim<-`, a matrix (usually double-precision) of coordinates, for each cell (row) and dimension (column). For `reducedDims<-`, a named SimpleList object containing such matrices. For `reducedDimNames<-`, a character vector containing the names of all dimensionality reduction results.

Details

Dimensionality reduction is often used to interpreting the results of single-cell data analysis. These methods allow the results of dimensionality reduction methods to be stored in a SingleCellExperiment object. Multiple results can be stored in a single object by assigning to different type in reducedDim<-.

If value is NULL for reducedDim<-, the set of results corresponding to type is removed from the object. If value is NULL for reducedDims<-, all dimensionality reduction results are removed.

Note that the reducedDims slot must always be named for consistency. Unnamed results assigned via reducedDim<- or reducedDims<- will be assigned empty names.

Value

For reducedDim, a numeric matrix is returned containing coordinates for cells (rows) and dimensions (columns).

For reducedDims, a named SimpleList of matrices is returned, with one matrix for each type of dimensionality reduction method.

For reducedDimNames, a character vector containing the names of the elements in reducedDims.

For reducedDim<- and reducedDims<-, a SingleCellExperiment object is returned with updated results in the reducedDims slot.

Author(s)

Aaron Lun

Examples

example(SingleCellExperiment, echo=FALSE)
reducedDim(sce, "PCA")
reducedDim(sce, "tSNE")
reducedDims(sce)

reducedDim(sce, "PCA") <- NULL
reducedDims(sce)

reducedDims(sce) <- SimpleList()
reducedDims(sce)

[Package SingleCellExperiment version 1.6.0 Index]