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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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copy number signature extraction - try to decompose to published CNV signature #136

Closed ipstone closed 2 years ago

ipstone commented 2 years ago

Congratulations on the new CNV signature paper! https://www.nature.com/articles/s41586-022-04738-6

I would like to extract CNV signatures (decompose to the published CNV signatures to get insights of the tumors) - for which I guess the right tool would be either using https://github.com/AlexandrovLab/SigProfilerSingleSample or SigProfilerExtractor?

Here are my more specific questions:

  1. For SigProfileSingleSample, I couldn't find the code to run it with CNV signatures - is there a way to run SigProfileSS using given signatures such as copy number signatures?

  2. For SigProfilerExtractor, I know for SNV, the extract signatures will be further decomposed into known/cosmic signatures. Will CNV signatures will be also decomposed? What are the main differences between these 'decomposed' activities vs. results from SigProfileSingleSample?

Thanks a lot!

marcos-diazg commented 2 years ago

Dear @ipstone,

Thanks so much for your interest and your kind words! Regarding your questions:

  1. If you want to perform mutational signature refitting analysis, we strongly recommend using our new SigProfilerAssignment tool, since we are in the process of retiring SigProfilerSingleSample. Just make sure to use the latest version of the tool, v0.0.8, which includes support for the current set of reference CNV signatures.

  2. In case you want to perform mutational signature de novo extraction and decomposition to COSMIC signatures, SigProfilerExtractor also supports CNV reference signatures.

If you want to learn more about the differences between the two types of analysis (de novo extraction vs. refitting), I would recommend checking the following references: https://doi.org/10.1016/j.mam.2019.05.002 or https://doi.org/10.1093/bib/bbx082.

I hope this helps, and please reopen the ticket if you have further questions.