convert_sigs_to_ref {MutationalPatterns} | R Documentation

## Convert tissue specific signature exposures to reference

### Description

This function converts tissue specific signature contributions into reference signature contributions. This works on SNV signatures from SIGNAL. It uses a conversion matrix to do the conversion. The output can include possible artifact signatures.

### Usage

    convert_sigs_to_ref(fit_res)

### Arguments

`fit_res` | Named list with signature contributions and reconstructed mutation matrix

### Value

The input fit_res, but with converted signature contributions.

### 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 tissue specific signatures
    signatures <- get_known_signatures(source = "SIGNAL", sig_type = "tissue", tissue_type = "Skin")

    ## Fit tissue specific signatures
    fit_res <- fit_to_signatures(mut_mat, signatures)

    ## Convert the tissue specific signatures exposures to reference
    fit_res <- convert_sigs_to_ref(fit_res)

[Package MutationalPatterns version 3.0.1 Index]