onset.est: Estimates inclusion times of genes in a correlated module

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

Description

Estimates inclusion times of genes in a correlated module

Usage

onset.est(ppt, mapping = 1, geneset, nodes, expr, alp = 20, w = 40,
  step = 10, do.perm = FALSE, winperm = 30, n.cells = 280,
  permut.n = 10, n.cores = 1, autocor.cut = 0.95, iterations = 15)

Arguments

ppt	ppt tree
mapping	id of probabilistic cells project to use
geneset	a set of genes that form a module
nodes	tips of a tree that form subtree (e.g, trajectory or fork)
expr	expression matrix
alp	parameter regulating stringency of inclusion event
w	local window of cells along pseudotime to estimate local correlation
step	shift of a window along pseudotime in number of cells
do.perm	do local estimates for locally permuted expression matrix
winperm	number of local cells for permutations
n.cells	total number of cells to consider from root in progenitor branch
permut.n	of local cells for permutations
n.cores	number of cores to calculate permutations used to estimate background local correlations in onset.est
autocor.cut	cutoff on correlation of inclusion times between sequential iterations of the algorithm to stop it
iterations	maximum number of iterations of the algorithm

Value

vector of inclusion times of genes

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