CaveatsΒΆ

Signature computation is performed using all mutations in your input file, not only the ones that map to the region of interest.

If the scores files lacks scores for some positions or certain alterations, OncodriveFML ignores them.

If, for any reason, your signatures lack certain triplets (probability equal to 0) that are the only ones present in certain region, OncodriveFML will not compute a P-value for that region.

OncodriveFML statistical power is limited by the number of simulations performed in each regions. You can increase the number of simulations, but be aware that the time cost is exponential.

Indels do not contribute to the signatures. You can simulate indels as substitutions and perform the simulations taking the signatures into account, but be aware that the signatures are not calculated considering indels.

Depending on the values of sampling_min_obs and sampling_chunk in the configuration file the number of simulations performed for a particular genomic element can differ.