cluster_signatures: Signature clustering function

View source: R/cluster_signatures.R

cluster_signaturesR Documentation

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)

UMCUGenetics/MutationalPatterns documentation built on Nov. 24, 2022, 4:31 a.m.