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mritchielab / FLAMES

A framework for performing single-cell and bulk read full-length analysis of mutations and splicing.
https://mritchielab.github.io/FLAMES/
GNU General Public License v3.0
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Mutation function #10

Closed mcortes-lopez closed 7 months ago

mcortes-lopez commented 1 year ago

Hi, I was trying to run the mutation function (sc_mutations), just changing the coverage min to 5, but I keep having the following error after some chromosomes:

Error in py_call_impl(callable, dots$args, dots$keywords) : ZeroDivisionError: float division by zero Calls: sc_mutations ... do.call -> <Anonymous> -> <Anonymous> -> py_call_impl

Given that there is not much information in the vignette, I was wondering if you would have a suggestion on how to debug this error?
Why is it 100 the minimum for the coverage used?

ChangqingW commented 1 year ago

Using 100 as the default threshold is probably because Luyi was working with deeper sequencing experiments, changing it to 5 should be fine. Could you try running the Python functions directly and see if it produce a more useful error message? sc_mutations is using the Python function in inst/Python/sc_mutations.py