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mutsigcv: how to assign categ in coverage table?
I am trying to figure out how to create my own coverage table for MutSigCV. However, I don't understand the meaning of "categ" in the context of the coverage table. Specifically, how are the labels "transition"/"transversion" assigned to an unmutated base in the genome?
My original hypothesis was that positions were contributing fractionally in a similar way as described for effect, i.e., any given base if mutated would give rise to a transversion 2/3 of the time and transition 1/3 of the time. However if this were the case, categ2 should be twice the value of categ1, categ4 twice categ3, and categ6 twice categ5. There seems to be a trend in this direction in the example file (LUSC.coverage.txt), but there is clearly more going on since the numbers are not exactly double, given the same gene and same "effect". I was hoping someone might be able to clarify.