slingPseudotime: Get Slingshot pseudotime values

In kstreet13/slingshot: Tools for ordering single-cell sequencing

Get Slingshot pseudotime values

Description

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

Usage

slingPseudotime(x, ...)

slingCurveWeights(x, ...)

slingAvgPseudotime(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, as.probs = FALSE)

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

## S4 method for signature 'ANY'
slingAvgPseudotime(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 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.

slingAvgPseudotime: a length n vector of average cell pseudotimes, where the average is a weighted average across lineages, weighted by the assignment weights.

Examples

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

kstreet13/slingshot documentation built on April 6, 2023, 11:12 p.m.