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

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

Description

Estimates inclusion times of genes in a correlated module for a number of probabilistic cell projections

Usage

onset(ppt, geneset, nodes = NULL, expr, alp = 20, w = 40,
  step = 10, n.cells = 280, mappings = 1, do.perm = FALSE,
  winperm = w, n.cores = parallel::detectCores()/2, permut.n = 10,
  n.cores1 = 1)

Arguments

ppt	ppt tree
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
n.cells	total number of cells to consider from root in progenitor branch
mappings	number of probabilistic cell projections to assess
do.perm	do local estimates for locally permuted expression matrix
winperm	number of local cells for permutations
n.cores	number of cores
permut.n	number of permutations used to estiamte background local correlations in onset.est
n.cores1	number of cores to calculate permutations used to estimate background local correlations in onset.est

Value

matrix of inclusion timing for each gene (rows) in each probabilistic cells projection (columns)

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