processRandomWalks: Process random walks into visitation frequency

In farrellja/URD: URD

Description

The output of simulateRandomWalk is vectors of cells visited by each random walk. This converts that data into the visitation frequency of each cell by the random walks, in addition to generating an independent pseudotime for that particular trajectory, which can be useful for some analyses.

Usage

processRandomWalks(
  object,
  walks,
  walks.name,
  aggregate.fun = mean,
  n.subsample = 10,
  verbose = T
)

Arguments

object	An URD object
walks	(List) List of character vectors of cells visited during random walks (i.e. the output of simulateRandomWalk)
walks.name	(Character) Name to use for storing walks
aggregate.fun	(Function) Function to aggregate pseudotime (default: mean)
n.subsample	(Numeric) Number of subsamplings to perform for calculating
verbose	(Logical) Report on progress

Value

An URD object with cell visitation frequency stored in @diff.data, a calculated pseudotime stored in @pseudotime, and subsampled data in @pseudotime.stability.

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