slingPseudotime {slingshot} | R Documentation

## Get Slingshot pseudotime values

### Description

Extract the matrix of pseudotime values or cells' weights along each lineage.

### Usage

    slingPseudotime(x, ...)

    slingCurveWeights(x, ...)

    ## S4 method for signature 'PseudotimeOrdering'
    slingPseudotime(x, na = TRUE)

    ## S4 method for signature 'SingleCellExperiment'
    slingPseudotime(x, na = TRUE)

    ## S4 method for signature 'SlingshotDataSet'
    slingPseudotime(x, na = TRUE)

    ## S4 method for signature 'PseudotimeOrdering'
    slingCurveWeights(x, as.probs = FALSE)

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

    ## S4 method for signature 'SlingshotDataSet'
    slingCurveWeights(x, as.probs = FALSE)

### Arguments

`x` | an object containing `slingshot` output.
`...` | additional parameters to be passed to object-specific methods.
`na` | logical. If `TRUE` (default), cells that are not assigned to a lineage will have a pseudotime value of `NA`. Otherwise, their arclength along each curve will be returned.
`as.probs` | logical. If `FALSE` (default), output will be the weights used to construct the curves, appropriate for downstream analysis of individual lineages (ie. a cell shared between two lineages can have two weights of `1`). If `TRUE`, output will be scaled to represent probabilistic assignment of cells to lineages (ie. a cell shared between two lineages will have two weights of `0.5`).

### Value

`slingPseudotime`: an `n` by `L` matrix representing each cell's pseudotime along each lineage.

`slingCurveWeights`: an `n` by `L` matrix of cell weights along each lineage.

### Examples

    data("slingshotExample")
    rd <- slingshotExample$rd
    cl <- slingshotExample$cl
    pto <- slingshot(rd, cl, start.clus = '1')
    slingPseudotime(pto)
    slingCurveWeights(pto)

[Package slingshot version 2.0.0 Index]