cluster_signatures: Signature clustering function

In CuppenResearch/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Signature clustering function

Description

Hierarchical clustering of signatures based on cosine similarity

Usage

cluster_signatures(signatures, method = "complete")

Arguments

signatures	Matrix with 96 trinucleotides (rows) and any number of signatures (columns)
method	The agglomeration method to be used for hierarchical clustering. This should be one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). Default = "complete".

Value

hclust object

See Also

plot_contribution_heatmap

Examples

## Get signatures
signatures <- get_known_signatures()

## See the 'mut_matrix()' example for how we obtained the mutation matrix:
mut_mat <- readRDS(system.file("states/mut_mat_data.rds",
  package = "MutationalPatterns"
))


## Hierarchically cluster the cancer signatures based on cosine similarity
hclust_signatures <- cluster_signatures(signatures)

## Plot dendrogram
plot(hclust_signatures)

CuppenResearch/MutationalPatterns documentation built on Nov. 23, 2022, 4:13 a.m.