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 'SlingshotDataSet'
    slingPseudotime(x, na = TRUE)

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

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

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

### 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 that sum to `1`).

### Value

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

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

### Methods (by class)

- `SlingshotDataSet`: returns the matrix of pseudotime values from a `SlingshotDataSet` object.

- `SingleCellExperiment`: returns the matrix of pseudotime values from a `SingleCellExperiment` object.

- `SlingshotDataSet`: returns the matrix of cell weights along each lineage from a `SlingshotDataSet` object.

- `SingleCellExperiment`: returns the matrix of cell weights along each lineage from a `SingleCellExperiment` object.

### Examples

    data("slingshotExample")
    rd <- slingshotExample$rd
    cl <- slingshotExample$cl
    sds <- slingshot(rd, cl)
    slingPseudotime(sds)
    data("slingshotExample")
    rd <- slingshotExample$rd
    cl <- slingshotExample$cl
    sds <- slingshot(rd, cl)
    slingCurveWeights(sds)

[Package slingshot version 1.5.1 Index]