I have two questions about how to compute the MutSigCV mutation table's categ values:
The documentation mentions that if this field is not specified in the existing maf, it can be computed using the pre-processing function of MutSigCV. However, no information is provided on how to execute this pre-processing function. What is the command-line for the pre-processing step, and what are the (minimal) input arguments/files?
In some cases, I have maf files that include sequence information on sites flanking the somatic mutations. In these instances, I can compute the categ values myself, but to do so, I need to be consistent in what is defined as a CpG transition/transversion. Does a CpG mutation (whether transition or transversion) only refer to mutations in the 5' cytosine, or in either the 5' cytosine or the 3' guanine?