readMAF | R Documentation |
Read mutation information from MAF file. For MAF format specification, see https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/.
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 = "",
...
)
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
|
if.parse.mutation.class |
if parse mutation class from mutation type
(variant classification) information. Default is |
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.
|
sep |
separator of columns. Default |
quote |
the set of quoting characters. To disable quoting altogether,
use |
... |
additional parameters pass to |
a data frame containing MAF information, plus optional columns of the parsed Mutation_Class and Protein_Position.
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