compscore: Compute StemID2 score

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

Compute StemID2 score

Description

This function extracts the number of links connecting a given cluster to other cluster, the delta median entropy of each cluster (median entropy of a cluster after subtracting the minimum median entropy across all clusters), and the StemID2 score which is the product of both quantities for each cluster.

Usage

compscore(object, nn = 1, scthr = 0, show = TRUE)

Arguments

object	Ltree class object.
nn	Positive integer number. Number of higher order neighbors to be included for the determination of links: indirect connections via n-1 intermittant neighbors are allowed. Default is 1.
scthr	Real number between zero and one. Score threshold for links to be included in the calculation. For scthr=0 all significant links are included. The maximum score is one.
show	logical. If TRUE, then plot heatmap of projections. Default is TRUE.

Value

A list ot three components:

links	a vector with the number of significant links for each cluster.
entropy	a vector with the delta entropy for each cluster.
StemIDscore	a vector with the StemID score for each cluster.

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