genotypeMatrix {maftools} | R Documentation

## Creates a Genotype Matrix for every variant

### Description

Creates a Genotype matrix using allele frequcies or by muatation status.

### Usage

    genotypeMatrix(
      maf,
      genes = NULL,
      tsb = NULL,
      includeSyn = FALSE,
      vafCol = NULL,
      vafCutoff = c(0.1, 0.75)
    )

### Arguments

`maf` | an `MAF` object generated by `read.maf`
`genes` | create matrix for only these genes. Define NULL
`tsb` | create matrix for only these tumor sample barcodes/samples. Define NULL
`includeSyn` | whether to include silent mutations. Default FALSE
`vafCol` | specify column name for vaf's. Default NULL. If not provided simply assumes all mutations are heterozygous.
`vafCutoff` | specify minimum and maximum vaf to define mutations as heterozygous. Default range 0.1 to 0.75. Mutations above maximum vafs are defined as homozygous.

### Value

matrix

### Examples

    laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
    laml <- read.maf(maf = laml.maf)
    genotypeMatrix(maf = laml, genes = "RUNX1")

[Package maftools version 2.4.12 Index]