Running cells with second-best SoS solution?

robertaboukhalil / ginkgo

Cloud-based single-cell copy-number variation analysis tool

qb.cshl.edu/ginkgo

BSD 2-Clause "Simplified" License

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Running cells with second-best SoS solution? #25

Closed laurenhummel closed 5 years ago

laurenhummel commented 5 years ago

Hi there,

I am using Gingko (CLI mostly) and am wondering if there is a way to re-run a small subset of cells to provide data from the second-best SoS solution? I have some cases where the least error and second least error are extremely close and I wish to look at certain cells/the output data under another copy number solution.

If not, could you point me to the appropriate place in the code to try making my own alterations? (Sorry, I am new to bioinformatics!!)

Thanks so much!

Lauren

robertaboukhalil commented 5 years ago

Hi Lauren,

Unfortunately Ginkgo doesn't currently support that, but if you'd like to modify the code, you would need to update this section of process.R.

Specifically, line 223 defines the value of CN. Currently, it says CN = CNmult[1,k], where the 1 in [1,k] means it uses the 1st least error for cell with ID k. I would start by stepping through that code to see if using [2,k] for example would help for a given cell k of interest.

Hope this helps!

Robert