fit_to_signatures {MutationalPatterns} | R Documentation

## Find optimal nonnegative linear combination of mutation signatures to reconstruct the mutation matrix.

### Description

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

### Usage

    fit_to_signatures(mut_matrix, signatures)

### Arguments

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

### Value

Named list with signature contributions and reconstructed mutation matrix

### See Also

`mut_matrix`,`fit_to_signatures_strict`,`fit_to_signatures_bootstrapped`

### Examples

    ## 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)

[Package MutationalPatterns version 3.0.1 Index]