Repository of the TRanslational ONCOlogy library, which includes various algorithms (such as CAPRESE and CAPRI) and the Pipeline for Cancer Inference (PICNIC).
In import.MAF, at line 110 there is a call to import.genotypes with parameter default.variant = "Mutation", however no such parameter exists in import.genotypes definition.
Same problem is raised in import.GISTIC.
Changing default.variant for event.type in the function call all seems to work so possibly this is the solution.
I've done a commit+push to solve the problem (basically implementing the solution I proposed), so check it.
Also modified ebind and sbind to apply a Reduce to input list instead of doing a for loop.
In import.MAF, at line 110 there is a call to import.genotypes with parameter default.variant = "Mutation", however no such parameter exists in import.genotypes definition. Same problem is raised in import.GISTIC. Changing default.variant for event.type in the function call all seems to work so possibly this is the solution.