clusterTree: Create hierarchical clustering trees for each cluster in a...

In treediff: Testing Differences Between Families of Trees

Create hierarchical clustering trees for each cluster in a given matrix

Description

This function creates a hierarchical clustering tree for each group in a given matrix. The function breaks the chromosome into clusters using the "broken stick" method and then converts the clusters into trees.

Usage

clusterTree(mat)

Arguments

mat	A matrix containing the data to cluster. It should have columns named 'index1', 'index2', 'chromosome and one column for each matrices.

Value

A list containing the following objects:

trees

A list of hierarchical clustering trees, one for each cluster in the matrix.

metadata

A data frame containing the following columns: names (name of each tree), chromosome, cluster, and file.

Examples

n <- 5

matrice <- matrix(runif(n*n), nrow = n, ncol = n)
matrice[lower.tri(matrice)] <- t(matrice)[lower.tri(matrice)]
matrice <- as.data.frame(matrice)
names(matrice) <- c("mat_1", "mat_2", "mat_3", "mat_4", "mat_5")

chromosome <- rep(1, n)
index1 <- sample(1:100, n, replace = TRUE)
index2 <- sample(1:100, n, replace = TRUE)

mat <- cbind(chromosome, index1, index2, matrice)

res <- clusterTree(mat)

treediff documentation built on May 29, 2024, 9:13 a.m.