divergencePreferenceDip: Calculate visitation divergence based on bimodality of...

In farrellja/URD: URD

Description

Calculates the preference of each cell for the two tips, tests for unimodality using Hartigan's dip test, and if unimodal, tests the mean to make sure that it's

Usage

divergencePreferenceDip(
  visit.data,
  cells.in.windows,
  cells.segment.1,
  cells.segment.2
)

Arguments

visit.data	(data.frame) Rows are cells, columns are: "segment.1" and "segment.2" (visitation frequency from random walks initiated in segment 1 and 2), "pseudotime" (the pseudotime of each cell), and "pseudotime.group" (the number of the pseudotime bin each cell belongs to)
cells.in.windows	(List) List of character vectors, giving names of cells in each pseudotime window.
cells.segment.1	(Character vector) Cells in segment 1
cells.segment.2	(Character vector) Cells in segment 2

Value

(data.frame) Rows are pseudotime windows, columns are a numeric representation of whether (0 or 1) ("p"), pseudotime of cells in the window ("mean.pseudotime", "min.pseudotime", "max.pseudotime"), and number of cells considered from each segment ("cells.visited.seg1", "cells.visited.seg2")

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