fit_to_signatures: Find optimal nonnegative linear combination of mutation...
In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Description Usage Arguments Value See Also Examples

Find the linear combination of mutation signatures that most closely reconstructs the mutation matrix by solving the nonnegative least-squares constraints problem.

1	fit_to_signatures(mut_matrix, signatures)

`mut_matrix`	mutation count matrix (dimensions: x mutation types X n samples)
`signatures`	Signature matrix (dimensions: x mutation types X n signatures)

Named list with signature contributions and reconstructed mutation matrix

mut_matrix,fit_to_signatures_strict,fit_to_signatures_bootstrapped

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

## Get signatures
signatures <- get_known_signatures()

## Perform the fitting
fit_res <- fit_to_signatures(mut_mat, signatures)

## This will also work for indels and dbs.
## An example is given for indels

## Get The indel counts
## See 'count_indel_contexts()' for more info on how to do this.
indel_counts <- readRDS(system.file("states/blood_indel_counts.rds",
  package = "MutationalPatterns"
))

## Get signatures
signatures <- get_known_signatures("indel")

fit_to_signatures(indel_counts, signatures)