readMAF: Read MAF file
In g3viz: Interactively Visualize Genetic Mutation Data using a Lollipop-Diagram

readMAF

R Documentation

Read MAF file

Description

Read mutation information from MAF file. For MAF format specification, see https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/.

Usage

readMAF(
  maf.file,
  gene.symbol.col = "Hugo_Symbol",
  variant.class.col = c("Variant_Classification", "Mutation_Type"),
  protein.change.col = c("Protein_Change", "HGVSp_Short"),
  if.parse.aa.pos = TRUE,
  if.parse.mutation.class = TRUE,
  mutation.class.col = "Mutation_Class",
  aa.pos.col = "AA_Position",
  mutation.type.to.class.df = NA,
  sep = "\t",
  quote = "",
  ...
)

Arguments

`maf.file`	MAF file name. Gnuzipped input file allowed, with ".gz" file extension.
`gene.symbol.col`	Column name of Hugo gene symbols (e.g., TP53). Default Hugo_Symbol.
`variant.class.col`	Column name for variant class information (e.g., Missense_Mutation, Nonsense_Mutation). Default is the first match of Variant_Classification or Mutation_Type.
`protein.change.col`	Column name for protein change information (e.g., p.K960R, G658S, L14Sfs15). Default is the first match of Protein_Change* or HGVSp_Short.
`if.parse.aa.pos`	if parse amino-acid position of mutations. Default is `TRUE`.
`if.parse.mutation.class`	if parse mutation class from mutation type (variant classification) information. Default is `TRUE`.
`mutation.class.col`	Column name of the parsed mutation class. Default Mutation_Class.
`aa.pos.col`	Column name of the parsed amino-acid change position. Default AA_Position.
`mutation.type.to.class.df`	mapping table from mutation type to class. `mapMutationTypeToMutationClass` for details. Default `NA`, which indicates to use default mappoings.
`sep`	separator of columns. Default `sep = "\t"`.
`quote`	the set of quoting characters. To disable quoting altogether, use `quote = ""`. Default `quote = ""`.
`...`	additional parameters pass to `read.table`.