Fitting somatic signatures to alexandrovs's
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@jolligoodfellow-9870
Last seen 5.8 years ago

Dear Bioconductor community,

I am succesfully using the bioconductor somatic signatures package on TCGA data but now i have the following problem:

I dont know how its possible to fit my results from sca_motifs in such manner that i get the best possible fit to Alexandrovs 30 classic signatures.

I hope someone can help me.


Greetings,

Jolli

 

 

somaticsignatures somaticsignatures mutationcontext • 741 views
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Julian Gehring ★ 1.3k
@julian-gehring-5818
Last seen 2.7 years ago

If you want to assess how similar signatures in your data are to a set of known signatures, for examples the ones published by Alexandrov and colleagues, you can first estimate the signatures from the data and then compute the similarity between the two sets of signatures. The idea is discussed in another thread: SomaticSignatures: Compare my datas with validated mutational signatures. Generally, you can retrieve the estimated signatures after a fit with signatures(object).

Directly considering a set of known signatures in the matrix decomposition is not an implemented high-level feature of the SomaticSignatures package. One can utilise the low-level functionality of the package for this. Can you describe your use case in a bit more detail? Then we can see how this might be possible to compute.

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