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Construct a Phylogenetic Tree from a Copy Number Variation (CNV) Matrix

CNVtree.Rd

This function constructs a phylogenetic tree based on a given copy number variation (CNV) matrix. It adds a baseline "Normal" profile only to root the tree, which is not shown in final output. First, it computes pairwise distances between profiles using Euclidean distance, and then applies a specified tree-building function (e.g., Neighbor-Joining) to construct the tree.

Usage

CNVtree(cnv_matrix, tree_function = nj)

Arguments

cnv_matrix

A matrix representing copy number variation, where rows correspond to samples and columns correspond to genomic regions. Each value represents the CNV at a given region in a sample.

tree_function

A function to construct the phylogenetic tree from a distance matrix. The default is nj (Neighbor-Joining). Other functions (e.g., upgma, wpgma) can also be used.

Value

A rooted phylogenetic tree (of class phylo)

Examples

# Example usage with Neighbor-Joining (default)