cos_sim_matrix: Compute all pairwise cosine similarities between mutational...

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

Compute all pairwise cosine similarities between mutational profiles/signatures

Description

Computes all pairwise cosine similarities between the mutational profiles provided in the two mutation count matrices. The cosine similarity is a value between 0 (distinct) and 1 (identical) and indicates how much two vectors are alike.

Usage

cos_sim_matrix(mut_matrix1, mut_matrix2)

Arguments

mut_matrix1	mutation count matrix (dimensions: a mutation features X n samples)
mut_matrix2	96 mutation count matrix (dimensions: a mutation features X m samples)

Value

Matrix with pairwise cosine similarities (dimensions: n mutational profiles X m mutational profiles)

See Also

mut_matrix, fit_to_signatures, plot_cosine_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"
))


## Calculate the cosine similarity between each COSMIC signature and each 96 mutational profile
cos_sim_matrix(mut_mat, signatures)

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