floodPseudotimeProcess: Process Flood Pseudotime

In farrellja/URD: URD

Description

This processes the values returned by floodPseudotime and stores the result as a pseudotime in an URD object.

Usage

floodPseudotimeProcess(
  object,
  floods,
  floods.name = "pseudotime",
  max.frac.NA = 0.4,
  pseudotime.fun = mean,
  stability.div = 10
)

Arguments

object	An URD object
floods	(data.frame) A data.frame of flood visitation information, returned by floodPseudotime
floods.name	(Character) The name to use for this pseudotime.
max.frac.NA	(Numeric) Maximum fraction of simulations that assigned NA for a cell. Cells with more NAs will not be assigned a pseudotime.
pseudotime.fun	(Function) Function to combine pseudotimes resulting from each simulation. Default (and only validated function) is mean.
stability.div	(Numeric) Number of simulation subsamplings to calculate.

Details

Several separate outputs from floodPseudotime can be combined using cbind and processed simultaneously. After calculation, pseudotimePlotStabilityOverall can be used to determine whether cell pseudotimes have stabilized with the number of simulations currently performed.

Value

An URD object with pseudotime stored in @pseudotime under the column name given in floods.name, with subsampling information stored in @pseudotime.stability. The information stored in @pseudotime.stability will be overwritten by any future pseudotime processing.

Examples

# Define the root cells as cells in HIGH stage
root.cells <- rownames(object@meta)[object@meta$STAGE == "ZFHIGH"]
# Do the simulation
flood.result <- floodPseudotime(object, root.cells = root.cells, n = 10, minimum.cells.flooded = 2, verbose = T)
# Convert to pseudotime in the URD object
object <- floodPseudotimeProcess(object, flood.result, floods.name = "pseudotime", max.frac.NA = 0.4, pseudotime.fun = mean, stability.div = 5)

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