collapseShortSegments: Collapse Short Segments

In farrellja/URD: URD

Description

This refines the dendrogram structure found by URD by removing overly short segments. It is automatically called by buildTree, but can be re-run if needed.

Usage

collapseShortSegments(
  object,
  min.cells.per.segment = 1,
  min.pseudotime.per.segment = 0.01,
  collapse.root = F
)

Arguments

object	An URD object
min.cells.per.segment	(Numeric) Remove segments with fewer cells assigned
min.pseudotime.per.segment	(Numeric) Remove segments shorter than this in pseudotime
collapse.root	(Logical) Is the very root most segment OK to delete? (Sometimes it would have no segments, but be important not to collapse)

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