search

broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
160 stars 87 forks source link

Documentation: explain how to extract information from the alternative solutions #67

Closed lbeltrame closed 4 years ago

lbeltrame commented 4 years ago

I have one case where I think that ichorCNA's best solution isn't the right one (as far as I can see the CN values are too shifted) but one of the alternative solutions fits the scenario better (with a very close log likelihood). Given that outputs are only selected for the optimal solution, I assume the RData files created by ichorCNA would contain what's needed. However there are a load of variables defined in them, so I'm not sure which one contains the data I require.

gavinha commented 4 years ago

Hi @lbeltrame

Obviously long over-due, but if you are still wondering, you can get it from the results list object. loglik data.frame will indicate the solutions.

In general, I usually re-run from the command-line but change --normal and --ploidy to the desired solution.

Best, Gavin