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)

## 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.

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)

Examples

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

[Package slingshot version 1.2.0 Index]