reducedDims: Reduced dimensions methods

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Methods to get or set the dimensionality reduction results.

Usage

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## S4 method for signature 'SingleCellExperiment,character'
reducedDim(x, type)

## S4 method for signature 'SingleCellExperiment,numeric'
reducedDim(x, type)

## S4 method for signature 'SingleCellExperiment,missing'
reducedDim(x, type)

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

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

## S4 replacement method for signature 'SingleCellExperiment'
reducedDims(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.

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.

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.

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

Author(s)

Aaron Lun

See Also

SingleCellExperiment-class

Examples

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

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

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

Bioconductor-mirror/SingleCellExperiment documentation built on July 15, 2017, 12:01 a.m.