explained_by_signatures {MutationalPatterns}R Documentation

This function has been renamed to 'cos_sim_matrix'.

Description

This function has been renamed to 'cos_sim_matrix'.

Usage

explained_by_signatures(mut_matrix, signatures)

Arguments

mut_matrix

96 mutation count matrix (dimensions: 96 mutations X n samples)

signatures

96 mutation count matrix (dimensions: 96 mutations X m samples)

Value

Matrix with pairwise cosine similarities

See Also

cos_sim_matrix mut_matrix, fit_to_signatures, plot_cosine_heatmap

Examples

## You can download mutational signatures from the COSMIC database:
# sp_url = http://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt
# cancer_signatures = read.table(sp_url, sep = "\t", header = T)

## We copied the file into our package for your convenience.
filename <- system.file("extdata/signatures_probabilities.txt",
                        package="MutationalPatterns")
cancer_signatures <- read.table(filename, sep = "\t", header = TRUE)

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

## Match the order to MutationalPatterns standard of mutation matrix
order = match(row.names(mut_mat), cancer_signatures$Somatic.Mutation.Type)
## Reorder cancer signatures dataframe
cancer_signatures = cancer_signatures[order,]
## Use trinucletiode changes names as row.names
## row.names(cancer_signatures) = cancer_signatures$Somatic.Mutation.Type
## Keep only 96 contributions of the signatures in matrix
cancer_signatures = as.matrix(cancer_signatures[,4:33])
## Rename signatures to number only
colnames(cancer_signatures) = as.character(1:30)

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


[Package MutationalPatterns version 2.0.0 Index]