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friend1ws / pmsignature

R package for extracting mutation signatures from a list of somatic mutations
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Can you please elaborate on the Simulated data #23

Closed Rashesh7 closed 7 months ago

Rashesh7 commented 7 years ago

Hi,

Can you please elaborate on how you generated the simulated data? For example, if you use K=3 while simulating the data, which 3 signatures are being used? And what are the ranges for alpha and gamma parameters. I am trying to compare a few tools including pmsignature and looking for a simulated data.

friend1ws commented 7 years ago

Hi,

Thanks for the interest in our package. Do you mean the simulation in the paper? The script used in the paper is at: https://github.com/friend1ws/pmsignature_paper/blob/master/analysis/simulation/script/runall.sh

Hope this helps for you.

Rashesh7 commented 7 years ago

Hi, Yes, the simulations used in the paper. Thank you for pointing me to the script. I had additional question, I am sorry if it is explicit somewhere, but when you mention True signature, are these from a specific file? or are you using the Cosmic Signatures as the base to simulate samples?

friend1ws commented 7 years ago

In this simulation, the signatures are generated from scratch by a probabilistic model (products of gamma distribution), and have no relationship with Cosmic Signatures.

Rashesh7 commented 7 years ago

Oh Ok, then does the tool have the capability of using an input set of signatures to make simulations?

friend1ws commented 7 years ago

No. We currently do not support that. For that experiment, you need to generate the set of mutations from e.g. COSMIC signatures with some probabilistic model by yourself.

Rashesh7 commented 7 years ago

Hi, Can you please elaborate on the Mutation Feature Vector Format for the type = "full" format

In the README you have described the format for type = "independent", right?

Basically, I have a file for 21 tumor samples (21 x 96) with number of mutations for each mutation context. Is there are way to directly use that kind of format?