Dear deconstructSigs user,

I have a question relating to the normalization parameter (tri.counts.method):

sample_1 = whichSignatures(tumor.ref = sigs.input, 
                           signatures.ref = signatures.nature2013, 
                           sample.id = 1, 
                           contexts.needed = TRUE,
                           tri.counts.method = 'default')

I have data from whole genome sequencing so should I set this parameter to 'genome' instead of 'default?

I try several options and the output is quite different.

Thank you for your help,

Bastien Nguyen