pseudotimeMovingWindow: Moving window through pseudotime

In farrellja/URD: URD

Description

Generates lists of cells using a moving window. Size of windows is either determined by pseudotime (if pseudotime.per.window is set) or by number of cells (if cells.per.window is set). If both are set, windows are determined by number of cells, but then windows whose pseudotime differ by less than pseudotime.per.window are collapsed.

Usage

pseudotimeMovingWindow(
  object,
  pseudotime,
  cells,
  moving.window,
  cells.per.window = NULL,
  pseudotime.per.window = NULL,
  name.by = c("mean", "min", "max")
)

Arguments

object	A URD object
pseudotime	(Character) Name of column in @pseudotime to use for pseudotime
cells	(Character vector) Names of cells to include
moving.window	(Numeric) Number of bins to use per window
cells.per.window	(Numeric or NULL) Size of bins (number of cells)
pseudotime.per.window	(Numeric or NULL) Size of bins (pseudotime)
name.by	(Character: "mean", "min", or "max")

Value

List of windows of cells, named by either the mean, min, or max pseudotime of those cells (depending on name.by).

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