fitTree: Fit tree using input parameters

In YosefLab/VISION: Functional interpretation of single cell RNA-seq latent manifolds

Fit tree using input parameters

Description

Fit tree using input parameters

Usage

fitTree(expr, nNodes, sigma, gamma, tol, maxIter)

Arguments

expr	Data to fit (NUM_GENES x NUM_SAMPLES)
nNodes	Number of nodes in the fitted tree, default is square-root of number of data points
sigma	Regularization parameter for soft-assignment of data points to nodes, used as the variance of a gaussian kernel. If 0, this is estimated automatically.
gamma	Graph-level regularization parameter, controlling the tradeoff between the noise-levels in the data and the graph smoothness. If 0, this is estimated automatically
tol	Tolerance to use when fitting the tree
maxIter	Maximum number of Iterations ot run the algorithm for

Value

(list) Tree characteristics:

• C spatial positions of the tree nodes in NUM_PROTEINS dimensional space

• unweighted (binary) adjacency matrix

• the mean-squared error of the tree

YosefLab/VISION documentation built on Feb. 19, 2023, 9:50 p.m.