allSegmentDivergenceByPseudotime: All Segment Divergence By Pseudotime

In farrellja/URD: URD

Description

All Segment Divergence By Pseudotime

Usage

allSegmentDivergenceByPseudotime(
  object,
  pseudotime,
  segments,
  divergence.method = c("ks", "preference"),
  pseudotime.cuts = 80,
  window.size = 5,
  minimum.visits = 10,
  visit.threshold = 0.7,
  p.thresh = 0.01,
  pref.thresh = 0.5,
  breakpoint.decision.plots = NULL,
  cache = T,
  verbose = F
)

Arguments

object	An URD object
pseudotime	(Character) Name of pseudotime to use for determining pseudotime of breakpoints
segments	(Character vector) Segments to consider fot determining visit divergence
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.
minimum.visits	(Numeric) Minimum number of random walk visits to a cell to retain it in the tree
visit.threshold	(Numeric) Cells are considered potential members for segments/tips from which random walks visited them at least this fraction of their maximum visitation from a single tip
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"
breakpoint.decision.plots	(Path) Path to save plots summarizing (default is NULL, which does not save plots as they are somewhat slow)
cache	(Logical) Used cached values? This will check object@tree$segment.divergence and only calculate values for new segments.
verbose	(Logical) Report on progress?

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