floodBuildTM: Build pseudotime transition matrix

In farrellja/URD: URD

Description

This scales the transition probabilities so that maximum sum of transition probabilities for a cell is 1. This modified matrix is used for calculating pseudotime. It requires either the user to provide an URD object (object=) with a diffusion map stored in slot @dm, or a diffusion map directly (dm=).

Usage

floodBuildTM(object = NULL, dm = NULL)

Arguments

object	An URD object
dm	A Diffusion Map

Details

This function can be called directly and the transition matrix stored, or floodPseudotime will call this function automatically if one isn't provided.

Thanks to @diegomscoelho for suggested improvements.

Value

A sparse matrix (dgCMatrix) of normalized transition probabilities.

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