SlingshotDataSet {slingshot} | R Documentation

## Extract Slingshot output

### Description

This is a convenience function to extract a `SlingshotDataSet` from an object containing `slingshot` output. However, we now recommend using a `PseudotimeOrdering` object, in most cases. The `SlingshotDataSet` is, however, still used for plotting purposes.

### Usage

    SlingshotDataSet(data, ...)

    ## S4 method for signature 'SingleCellExperiment'
    SlingshotDataSet(data)

    ## S4 method for signature 'SlingshotDataSet'
    SlingshotDataSet(data)

    ## S4 method for signature 'PseudotimeOrdering'
    SlingshotDataSet(data)

### Arguments

`data` | an object containing `slingshot` output.
`...` | additional arguments to pass to object-specific methods.

### Value

A `SlingshotDataSet` object containing the output of `slingshot`.

### See Also

`PseudotimeOrdering`, `as.SlingshotDataSet`

### Examples

    data("slingshotExample")
    rd <- slingshotExample$rd
    cl <- slingshotExample$cl
    library(SingleCellExperiment)
    u <- matrix(rpois(140*50, 5), nrow = 50)
    sce <- SingleCellExperiment(assays = list(counts = u),
                                reducedDims = SimpleList(PCA = rd),
                                colData = data.frame(clus = cl))
    sce <- slingshot(sce, clusterLabels = 'clus', reducedDim = 'PCA')
    SlingshotDataSet(sce)

[Package slingshot version 2.2.1 Index]