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_Class"),
  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", ...)

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 of variant class information (e.g., Missense_Mutation, Nonsense_Mutation). Default is a list of Variant_Classification and Mutation_Class.

protein.change.col

Column name of protein change information (e.g., p.K960R, G658S, L14Sfs*15). Default is a list of Protein_Change, 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".

...

additional parameters pass to read.table.

Value

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