mutCountMatrix {maftools} | R Documentation

## Generates count matrix of mutations.

### Description

Generates a count matrix of mutations. i.e, number of mutations per gene per sample.

### Usage

    mutCountMatrix(
      maf,
      includeSyn = FALSE,
      countOnly = NULL,
      removeNonMutated = TRUE
    )

### Arguments

`maf` | an MAF object generated by `read.maf`
`includeSyn` | whether to include sysnonymous variants in ouput matrix. Default FALSE
`countOnly` | Default NULL - counts all variants. You can specify type of 'Variant_Classification' to count. For e.g, countOnly = 'Splice_Site' will generates matrix for only Splice_Site variants.
`removeNonMutated` | Logical Default `TRUE`, removes samples with no mutations from the matrix.

### Value

Integer Matrix

### See Also

`getFields` `getGeneSummary` `getSampleSummary`

### Examples

    laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
    laml <- read.maf(maf = laml.maf)
    ##Generate matrix
    mutCountMatrix(maf = laml)
    ##Generate count matrix of Splice_Site mutations
    mutCountMatrix(maf = laml, countOnly = 'Splice_Site')

[Package maftools version 2.10.05 Index]