Hi,

I am a researcher using The Cancer Genome Atlas. I would like to use capri but am new to all bioconductor packages. It says i need a TRONCO complaint dataset. What is a TRONCO compliant dataset? Is there a package that can make a .MAF file TRONCO complaint?

Thanks!

Hi,

sorry for the delay in answering this.

TRONCO has facilities to load MAF files has R data.frames; after that, you can manipulate the dataset (e.g., to remove duplicates) and then you can marshal it to a TRONCO dataset.  The CRC example on the TRONCO website (http://bimib.disco.unimib.it/index.php/Tronco) can give you a hint about all the things you can do.

Marco

Sorry to see this late. Check out function import.MAF -- that function scans a MAF file in the TCGA input format and transforms it in  TRONCO's internal representation.