Data files

input_data/

Files that do not get edited. Includes:

• NCI MAF file (tarred and gzipped), in NCI directory
• virusscan counts file (vscan_counts.tsv), for determining HPV status

output_data/

Analysis output files. Includes:

• MAFs after split, removing DNP, changing to hg19, etc
• trinucleotide context file from the main MAF with no HPV split.

Trinucleotide context file

You can load() this into R. It is a list structure, where:

• trinuc.contexts[[1]] gives you the summary used for the selection analysis (average of contexts)
• trinuc.contexts[[2]][[1]] gives you the output from the first tumor
• trinuc.contexts[[2]][[2]] gives the second, etc.

Analyses

The analysis for the manuscript is available in a markdown file here.