activation.fork: Estimate optimum of expression and time of activation

In hms-dbmi/crestree: Analysis of branching branching trajectories from single-cell data

Description

Estimate optimum of expression and time of activation

Usage

activation.fork(r, fork.de, mat, root, leaves, deriv.cutoff = 0.015,
  gamma = 1, n.mapping = 1, n.cores = parallel::detectCores()/2)

Arguments

r	ppt.tree object
fork.de	outcome of test.fork.genes function
mat	expression matrix
root	root of progenitor branch of bifurcation
leaves	leaves of derivative branches of bifurcation
deriv.cutoff	a first passage of derivative through cutoff 'deriv.cutoff' to predict activation timing
gamma	gamma parameter in gam function
n.mapping	results are averaged among n.mapping number of probabilsitic cell projections
n.cores	number of cores to use

Value

table fork.de with added per gene timing of optimum and activation

hms-dbmi/crestree documentation built on July 11, 2019, 8:04 p.m.