genotypeMatrix: Creates a Genotype Matrix for every variant
In maftools: Summarize, Analyze and Visualize MAF Files

Description Usage Arguments Value Examples

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

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

`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.

matrix

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