readMAF: 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 = "",
  ...
)

Value

a data frame containing MAF information, plus optional columns of the parsed Mutation_Class and Protein_Position.

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, L14Sfs*15). 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.