test.fork.genes: Determine genes differentially upregulated after bifurcation...

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

Description

Determine genes differentially upregulated after bifurcation point

Usage

test.fork.genes(r, mat, matw = NULL, root, leaves,
  genes = rownames(mat), n.mapping = 1, n.mapping.up = 1,
  n.cores = parallel::detectCores()/2)

Arguments

r	pptree object
mat	expression matrix of genes (rows) and cells (columnts)
root	a principal point of fork root
leaves	vector of two principal points of fork leaves
genes	optional set of genes to estimate association with fork
n.mapping	number of probabilistic cell-to-tree projections to use for robustness
n.mapping.up	number of probabilistic cell-to-tree projections to estimate the amount of upregulation relative to progenitor branch

Value

summary statistics of size effect and p-value of association with bifurcaiton fork.

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