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broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
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Detailed output of non-primary solutions #44

Open ivlachos opened 5 years ago

ivlachos commented 5 years ago

Hi,

Is there a way to access the detailed output of the non-primary solutions? It seems that only the figures in the pdf output are available.

Thanks!

gavinha commented 5 years ago

Hi @ivlachos

At the moment, sub-optimal solutions are not being output except for the genome-wide plots for inspection of the solutions. Following inspection, if we need to select another solution, we typically re-run using the desired initializations of normal contamination (e.g n0.85) and ploidy (e.g. p3). That being said, all the solutions are stored in the .RData object from the original run. The results variable is a list containing all the solutions as its elements. ind contain the indices for the ordering of the solutions in descending order. You can modify ichorCNA.R script to loop over the list and save all the files by using the same code to print out the single optimal solution.

Best, Gavin

ivlachos commented 5 years ago

Hi @gavinha,

I'll dive in the RData.

Thank you!