fit.associated.genes: Model gene expression levels as a function of tree positions.

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

Description

Model gene expression levels as a function of tree positions.

Usage

fit.associated.genes(r, X, n.map = 1,
  n.cores = parallel::detectCores()/2, method = "ts", knn = 1,
  gamma = 1.5)

Arguments

r	pptree object
X	expressinon matrix of genes (rows) vs cells (columns)
n.map	number of probabilistic cell-to-tree mappings to use
method	method of modeling. Currently only splines with option 'ts' are supported.
knn	use expression averaging among knn cells
gamma	stringency of penalty.

Value

modified pptree object with new fields r$fit.list, r$fit.summary and r$fit.pattern. r$fit.pattern contains matrix of fitted gene expression levels

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