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Question: Determining number of signatures in SomaticSignatures
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gravatar for chang02_23
2.6 years ago by
chang02_2320
United States
chang02_2320 wrote:

I have a 20 samples with mutations ranging from 50 to 144 to extract signatures. I don't find an inflection point to determine rank. It seems like the more ranks I use the "better" fit. i suppose with the small number of samples i have there really can't be more than 2 or 3 signatures. Also as i look at the samples contributing to the signatures, some have multiple similar signatures. 

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signature 5

ADD COMMENTlink modified 2.6 years ago by Julian Gehring1.3k • written 2.6 years ago by chang02_2320

Just to clarify, you have 20 different samples where the number of mutations per sample ranges from 50 to 144?

ADD REPLYlink written 2.6 years ago by Julian Gehring1.3k

Correct, 20 different samples.

ADD REPLYlink written 2.6 years ago by chang02_2320
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gravatar for Julian Gehring
2.6 years ago by
Julian Gehring1.3k
Julian Gehring1.3k wrote:

What you most likely see here is an effect of the mutation data itself. As you wrote, each of your samples has 50 to 114 mutations. This is a very low number of variants to infer general characteristics from. Consider that we have 96 possible motifs which means that each sample on average has around 1 variant per motif. You can have a look at this question for a detailed discussion of such cases: SomaticSignatures low mutation rates. Instead of trying to identify signatures on a per-sample base, you could try to define another relevant grouping and aggregate the variants by this groups. The case study covered in the vignette is using this approach, where signatures are estimated at the level of studies.

ADD COMMENTlink written 2.6 years ago by Julian Gehring1.3k
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