fitTree: Fit tree using input parameters

View source: R/TreeBasedMethods.R

fitTreeR Documentation

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 June 14, 2024, 5:27 p.m.