floodPseudotimeCalc: A single iteration of flood pseudotime calculation.

In farrellja/URD: URD

Description

This runs a single iteration of flood pseudotime. This function is meant to be called by floodPseudotime to run many iterations.

Usage

floodPseudotimeCalc(
  object,
  start.cells,
  minimum.cells.flooded = 2,
  tm.flood = NULL,
  verbose.freq = 0
)

Arguments

object	An URD object
start.cells	(Character vector) Cells to initialize as visited to start pseudotime calculation
minimum.cells.flooded	(Numeric) Stop pseudotime calculation when fewer cells are newly visited in a given iteration, and assign remaining unvisited cells pseudotime NA.
tm.flood	(Sparse or full matrix) A sparse matrix of normalized transition probabilities. If unprovided (NULL), this will be calculated automatically.
verbose.freq	(Numeric) Report progress after this many iterations. 0 is silent.

Value

(Numeric vector) The iteration that newly visited each cell.

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