piu_mapping: This function generates three files as the final products....
In ginnyintifa/GPD:

This function generates three files as the final products. First, each piu mapped, second, lu summarised per gene, third, npc summarised per gene.

1 2	piu_mapping(piu_df, pc_data_name, npc_data_name, cancer_barcode, output_dir)

`pc_data_name`	the file listing mutations that result in protein consequence. A file generated by function germline_extraction_annotation_pos
`npc_data_name`	the file listing mutations that result in non-protein consequence. A file generated by function germline_extraction_annotation_pos
`cancer_barcode`	Patient barcodes for this cancer type cohort.
`output_dir`	The directory you would like to have your output files in.
`piu_filename`	The file provided by the package where the piu information is recorded.

piu_mapping (piu_df = ptm_pfam_combine,
                     pc_data_name  =  "/Users/ginny/Google Drive/R_GPD/GPD_package_0401/example/example_mutation_pc_pos.tsv",
                     npc_data_name = "/Users/ginny/Google Drive/R_GPD/GPD_package_0401/example/example_mutation_npc.tsv",
                     cancer_barcode = sel_example_barcode,