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ShixiangWang / sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
https://shixiangwang.github.io/sigminer/
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optimal bootstrapping parameter #385

Closed joonan30 closed 3 years ago

joonan30 commented 3 years ago

Hi Shixiang,

Thanks for the nice tool. I am following the best practice for WES data. I got to the point for other parameters but not sure the bootstrapping parameter. I used 10 as the manual but is there any good recommendation for the bootstrapping parameter (e.g. by sample size)? I am using Sigminer for ~200 WES samples. Many thanks!

ShixiangWang commented 3 years ago

20 should be okay.

This function is a little Computation-intensive, you can reduce n_nmf_run to 30 when you want to reduce the running time.