Overview of Maftools package. Table headers describe available modules, namely, Visualization, Set operation, Variant annotations, and Analysis. A small description and the corresponding function (bold italics) in Maftools package are provided for every module. The typical workflow begins with MAF object creation either by reading an MAF file or by converting existing annotations to an MAF object, which is later passed to a desired function as an input (arrows). The visualization module includes functions to generate publication ready plots from the input MAF object, whereas the analysis module offers functions to perform commonly performed analyses in cancer genomics. The variant annotation module performs variant annotations using oncotator API and format conversion of annotations generated by programs such as ANNOVAR. The set operation includes function for subsetting MAF object based on user-defined queries.
