synchro: Estimates pseudotime trends of local intra- and inter-module...

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

Description

Estimates pseudotime trends of local intra- and inter-module correlations of fates-specific modules

Usage

synchro(ppt, fpm, root, leaves, genesetA, genesetB, w, step, n.mapping,
  n.points = 100, span.smooth = 0.1, perm = FALSE)

Arguments

ppt	ppt object
fpm	expression matrix
root	root of progenitor branch of bifurcation
leaves	leaves of derivative branches of bifurcation
genesetA	a vector of fate-specific genes for first post-bifurcation branch
genesetB	a vector of fate-specific genes for second post-bifurcation branch
w	local window, in number of cells, to estimate correlations
step	step, in number of cells, between local windows
n.mapping	number of probabilistic cells projection to use for estimates
n.points	number of pseudotime points to extrapolate and visualize patterns
span.smooth	smooth parameters of loess
perm	boolean, estimate control trends for local permutations instread of real expression matrix

Value

estimates of local correlation trend for each probabilistic cell projection and average among cell projections

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