averagePseudotime: Compute the average pseudotime

In LTLA/TrajectoryUtils: Single-Cell Trajectory Analysis Utilities

Compute the average pseudotime

Description

Compute the average pseudotime for each cell across all paths in which it is involved.

Usage

averagePseudotime(x, i = 1L)

Arguments

x	A numeric matrix-like object containing pseudotime orderings. Alternatively, a PseudotimeOrdering object containing such a matrix.
i	Integer scalar or string specifying the entry of pathStats(x) containing the pseudotime matrix, if x is a PseudotimeOrdering object.

Details

Averaging the pseudotime is a convenient way to consolidate multiple paths into a single ordering for, e.g., visualization. It is permissible as cells involved in multiple paths should generally have similar pseudotimes in each path, under assumption that the cell is involved in the part of the trajectory that is common to those paths. In such cases, the average is just a way of compressing those pseudotimes into a single value. Conversely, for cells that are unique to a single path, the average collapses to that path's pseudotime (assuming that all other values are NA).

Value

A numeric vector containing the average pseudotime for each cell.

Author(s)

Aaron Lun

Examples

pseudotimes <- matrix(rnorm(200), ncol=2)
pseudotimes[1:40,1] <- NA
pseudotimes[61:100,2] <- NA
pseudotimes[41:60,] <- runif(20)
averagePseudotime(pseudotimes)

pto <- PseudotimeOrdering(pseudotimes)
averagePseudotime(pto)

LTLA/TrajectoryUtils documentation built on Feb. 5, 2024, 11:56 a.m.