transitionProbs: Function for the computation of transition probabilities...

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

Function for the computation of transition probabilities between clusters

Description

This function computes transition probabilities between clusters based on the link probabilities of the pruned k nearest neighbour graph.

Usage

transitionProbs(res, cl, pvalue = 0.01)

Arguments

res	List object with k nearest neighbour information returned by pruneKnn function.
cl	List object with clustering information, returned by the graphCluster function. If an aggregated cluster of tiny clusters (singletons) exists, stored in residual.cluster, this cluster is disregarded, and no links with this clusters are inferred.
pvalue	Positive real number between 0 and 1. All nearest neighbours with link probability < pvalue are discarded. Default is 0.01.

Value

Matrix of transition probabilities between clusters.

Examples

res <- pruneKnn(intestinalDataSmall,knn=10,alpha=1,no_cores=1,FSelect=FALSE)
cl <- graphCluster(res,pvalue=0.01)
probs <-transitionProbs(res,cl,pvalue=0.01) 

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