search

AlexandrovLab / SigProfilerExtractorR

An R wrapper for SigProfilerExtractor that allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
BSD 2-Clause "Simplified" License
15 stars 2 forks source link

unexpected keyword argument 'collapse_to_SBS96' #13

Closed togasaki1220 closed 1 year ago

togasaki1220 commented 1 year ago

Hi,

I am trying to run the sigprofilerextractor() function as following:

sigprofilerextractor("vcf", output, inputdata, "GRCh37"

exome = TRUE #when WES turn TRUE

                 #minimum_signatures= 1,
                 #maximum_signatures= 25,
                 #nmf_replicates= 100,
                 #min_nmf_iterations = 10000,
                 #max_nmf_iterations =1000000,
                 #nmf_test_conv = 10000,
                 #nmf_tolerance = 0.00000001,

)

The type of inputdata file is vcf format.

I am having the following error when trying to run: Error in py_call_impl(callable, dots$args, dots$keywords) : TypeError: sigProfilerExtractor() got an unexpected keyword argument 'collapse_to_SBS96'

marcos-diazg commented 1 year ago

Dear @togasaki1220,

I have just transferred your issue to the appropriate repo, as you are asking about the sigprofilerextractor function.

Could you please check that you have the latest versions of both the SigProfilerExtractorR R wrapper (v1.1.16) and the associated SigProfilerExtractor python package (v1.1.20)?

marcos-diazg commented 1 year ago

Please let us know and reopen the ticket if you are still having this issue after updating the versions of SigProfilerExtractorR and SigProfilerExtractor. Thanks for your interest!