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AlexandrovLab / SigProfilerExtractor

SigProfilerExtractor 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
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number of signatures #138

Closed dmusachio closed 2 years ago

dmusachio commented 2 years ago

Hi,

I am setting the minimum number of signatures to be extracted to 5, yet in my decomposition plot, I only see one signature. Is this a bug or am I reading the plot below incorrectly?

Capture

The reason I am trying to extract more signatures is that I read that 5-10 signatures tends to create the highest cosine similarity and the lowest error rate.

Thanks

marcos-diazg commented 2 years ago

Dear @dmusachio,

Could you please confirm the number of samples that you are using to extract mutational signatures? Also, the number of signatures to extract is totally dependent on your dataset and the mutational processes shaping the mutations found in that specific cohort. SigProfilerExtractor will automatically select the more appropriate number of signatures.

marcos-diazg commented 2 years ago

Please reopen the ticket if you are still experiencing this issue. Thanks so much for your interest in our tool!