cellsfromtree: Extract Cells on Differentiation Trajectory

In RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Extract Cells on Differentiation Trajectory

Description

This function extracts a vector of cells on a given differentiation trajectory in pseudo-temporal order determined from the projection coordinates.

Usage

cellsfromtree(object, z)

Arguments

object	Ltree class object.
z	Vector of valid cluster numbers ordered along the trajectory.

Value

A list ot four components:

f	a vector of cells ids ordered along the trajectory defined by z.
g	a vector of integer number. Number i indicates that a cell resides on the link between the i-th and (i+1)-th cluster in z.

Examples

sc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)
sc <- compdist(sc)
sc <- clustexp(sc)
sc <- findoutliers(sc)
sc <- comptsne(sc)
ltr <- Ltree(sc)
ltr <- compentropy(ltr)
ltr <- projcells(ltr)
ltr <- lineagegraph(ltr)
ltr <- comppvalue(ltr)
x <- cellsfromtree(ltr,c(1,3,6,2))

RaceID documentation built on Sept. 28, 2023, 5:06 p.m.