as.PseudotimeOrdering {slingshot} | R Documentation

## Conversion to PseudotimeOrdering

### Description

This function converts objects that contain `slingshot` results into a `PseudotimeOrdering`.

### Usage

    as.PseudotimeOrdering(x, ...)

    ## S4 method for signature 'SlingshotDataSet'
    as.PseudotimeOrdering(x)

    ## S4 method for signature 'SingleCellExperiment'
    as.PseudotimeOrdering(x)

    ## S4 method for signature 'PseudotimeOrdering'
    as.PseudotimeOrdering(x)

### Arguments

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

### Value

A `PseudotimeOrdering` object containing the `slingshot` results from the original object, `x`.

### 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')
    as.PseudotimeOrdering(sce)

[Package slingshot version 2.2.1 Index]