clusterTipPotential: Tip Potential of Clusters

In farrellja/URD: URD

Description

Calculate likelihood that each cluster is a potential tip.

Usage

clusterTipPotential(
  object,
  pseudotime,
  clustering,
  name.store = "tip.potential"
)

Arguments

object	An URD object
pseudotime	(Character) Pseudotime to use (i.e. a column of @pseudotime)
clustering	(Character) Clustering to use (i.e. a column of @group.ids)
name.store	(Character) Name to store this tip potential calculation under (a column of @pseudotime)

Details

This assumes that clusters that are tips will be primarily connected to cells with younger pseudotime. Thus, this function calculates the pseudotime difference between each cell in the data and mean pseudotime of each cluster. Then, the pseudotime differences are averaged To do this, the cumulative transition probability from all cells in the cluster to all cells outside of the clusters is calculated. Then, the pseudotime difference between each cell and the mean of the cluster is calculated, and a weighted average is performed according to the cumulative transition probability.

Value

An URD object with a column in @pseudotime named according to name.store.

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.