branchcells: Differential Gene Expression between Links

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

Differential Gene Expression between Links

Description

This function computes expression z-score between groups of cells from the same cluster residing on different links

Usage

branchcells(object, br)

Arguments

object	Ltree class object.
br	List containing two branches, where each component has to be two valid cluster numbers seperated by a . and with one common cluster in the two components. The lower number precedes the larger one, i.e. 1.3. For each component, the cluster number need to be ordered in increasing order.

Value

A list ot four components:

n	a vector with the number of significant links for each cluster.
scl	a vector with the delta entropy for each cluster.
k	a vector with the StemID score for each cluster.
diffgenes	a vector with the StemID score for each cluster.

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 <- branchcells(ltr,list("1.3","3.6"))
head(x$diffgenes$z)
plotmap(x$scl)
plotdiffgenes(x$diffgenes,names(x$diffgenes$z)[1])

RaceID documentation built on April 4, 2025, 4:34 a.m.