slingLineages: Extract the Slingshot lineages

In slingshot: Tools for ordering single-cell sequencing

Description

Extract lineages (represented by ordered sets of clusters) identified by slingshot.

Usage

slingLineages(x)

## S4 method for signature 'SlingshotDataSet'
slingLineages(x)

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

Arguments

x	an object containing slingshot output.

Value

the list of lineages, represented by ordered sets of clusters.

Methods (by class)

• SlingshotDataSet: returns the list of lineages, represented by ordered sets of clusters from a SlingshotDataSet object.

• SingleCellExperiment: returns the list of lineages, represented by ordered sets of clusters from a SingleCellExperiment object.

Examples

data("slingshotExample")
rd <- slingshotExample$rd
cl <- slingshotExample$cl
sds <- getLineages(rd, cl)
slingLineages(sds)

Example output

Loading required package: princurve
Using full covariance matrix
$Lineage1
[1] "1" "2" "3" "5"

$Lineage2
[1] "1" "2" "3" "4"

slingshot documentation built on Nov. 8, 2020, 5:51 p.m.