visitDivergenceByPseudotime: Visitation Divergence for Pseudotime Windows

In farrellja/URD: URD

Description

Visitation Divergence for Pseudotime Windows

Usage

visitDivergenceByPseudotime(
  object,
  pseudotime,
  segment.1,
  segment.2,
  cells.in.segments = NULL,
  cells.segment.1 = NULL,
  cells.segment.2 = NULL,
  divergence.method = c("ks", "preference"),
  pseudotime.cuts = 80,
  window.size = 5,
  pseudotime.min = NULL,
  pseudotime.max = NULL,
  p.thresh = 0.01,
  pref.thresh = 0.5,
  verbose = T
)

Arguments

object	An URD object
pseudotime	(Character) Name of pseudotime to use for determining pseudotime of breakpoints
segment.1	(Character) First segment to compare (Not necessary if cells.in.segment.1 is set)
segment.2	(Character) Second segment to compare (Not necessary if cells.in.segment.2 is set)
cells.in.segments	(data.frame) Output from putativeCellsInSegments that describes which cells can belong to which segments. (Not necessary if cells.in.segment.1 and cells.in.segment.2 are both set)
cells.segment.1	(Character Vector) List of cells that belong to segment 1 for comparison (not necessary if segment.1 and cells.in.segments are provided, in which case set to NULL)
cells.segment.2	(Character Vector) List of cells that belong to segment 2 for comparison (not necessary if segment.2 and cells.in.segments are provided, in which case set to NULL)
divergence.method	(Character: "ks" or "preference") Test to use to determine whether visitation has diverged for each pseudotime window.
pseudotime.cuts	(Numeric) Approximate number of cells to assign to each pseudotime bin for branchpoint finding.
window.size	(Numeric) Width of moving window in pseudotime used for branchpoint finding, in terms of bins.
pseudotime.min	(Numeric) Minimum pseudotime of cells to compare
pseudotime.max	(Numeric) Maximum pseudotime of cells to compare
p.thresh	(Numeric) p-value threshold to use in determining whether visitation is significantly different from pairs of tips
pref.thresh	(Numeric) Maximum mean preference within a window to be considered 'different' if divergence.method=="preference"

Value

(List) Number of cells considered ("cells.considered"), the determined pseudotime breakpoint ("breakpoint"), and the details of the calculation for each window ("details"), which is a data.frame: Rows are pseudotime windows, columns are KS-test p-value adjusted for multiple hypotheses ("p"), pseudotime of cells in the window ("mean.pseudotime", "min.pseudotime", "max.pseudotime"), number of cells considered from each segment ("cells.visited.seg1", "cells.visited.seg2"), and whether the window passed the p-value threshold for significance ("different")

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