Using the information provided in the optional hotspots file of deepCSA, we could provide a computation of whether the (known) tumor hotspots are selected or not for each specific gene.
This could be done by taking the output of a site comparison process, and then also the file with the hotspots annotation, and with these two you could:
- Annotate whether each position is or is not a known hotspot.
- Group positions based on Gene and Hotspot(Yes/No). Apply the sum to the expected and observed columns independently.
- Perform 3 different groupings based on: site, amino acid change and amino acid, and for each of them...
- Compute the updated Obs/Exp ratios and the p-values in the same way as it is being done for the individual site selection computations.
- Apply multiple testing correction to the p-values.
For this we need to have a new nf module, a new python script and import some of the functions that are already present.
Using the information provided in the optional hotspots file of deepCSA, we could provide a computation of whether the (known) tumor hotspots are selected or not for each specific gene.
This could be done by taking the output of a site comparison process, and then also the file with the hotspots annotation, and with these two you could:
For this we need to have a new nf module, a new python script and import some of the functions that are already present.