extractSignatures {maftools} | R Documentation

## Extract mutational signatures from trinucleotide context.

### Description

Decompose a matrix of 96 substitution classes into `n` signatures.

### Usage

    extractSignatures(
      mat,
      n = NULL,
      plotBestFitRes = FALSE,
      parallel = 4,
      pConstant = NULL
    )

### Arguments

`mat` | Input matrix of diemnsion nx96 generated by `trinucleotideMatrix`
`n` | decompose matrix into n signatures. Default NULL. Tries to predict best value for `n` by running NMF on a range of values and chooses based on cophenetic correlation coefficient.
`plotBestFitRes` | plots consensus heatmap for range of values tried. Default FALSE
`parallel` | Default 4. Number of cores to use.
`pConstant` | A small positive value to add to the matrix. Use it ONLY if the functions throws an `non-conformable arrays` error

### Details

This function decomposes a non-negative matrix into n signatures.

### Value

a list with decomposed scaled signatures, signature contributions in each sample and NMF object.

### See Also

`trinucleotideMatrix` `plotSignatures` `compareSignatures`

### Examples

    ## Not run:
    laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
    laml <- read.maf(maf = laml.maf)
    laml.tnm <- trinucleotideMatrix(maf = laml, ref_genome = 'BSgenome.Hsapiens.UCSC.hg19', prefix = 'chr',
    add = TRUE, useSyn = TRUE)
    library("NMF")
    laml.sign <- extractSignatures(mat = laml.tnm, plotBestFitRes = FALSE, n = 2, pConstant = 0.01)

    ## End(Not run)

[Package maftools version 2.4.12 Index]