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im3sanger / dndscv

dN/dS methods to quantify selection in cancer and somatic evolution
GNU General Public License v3.0
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Very high dnds values #66

Closed ArashDepp closed 3 years ago

ArashDepp commented 3 years ago

Hi.

I ran dndscv with hg19 based cancer mutation data with default parameters. However, I am observing that dn/ds ratio is shooting very high. For example, here is the distribution for dnds for mis-sense mutations (i.e wmis) across all genes. I removed outliers which even go upto 25000. image

Even retaining only the genes with q-value of mis-sense mutations < 0.1 gives roughly the same distribution. Also the global estimate for mis-sense mutations is 450, which is way too higher than 1.

Could you help me to understand why this is the case? Appreciate your time and help.

ArashDepp commented 3 years ago

Okay. I found a similar question by another user and the possible reason could be the lack of synonymous mutations in the data. I will keep it open for now and if introducing synonymous mutations solve this problem, then I will close it :)

ArashDepp commented 3 years ago

Yes indeed, the issue was lack of synonymous mutations in the input file. A quick tip for those who might be using maftools: mafObject@data gives the nonsynonymous mutations mafObject@maf.silent gives the silent/synonymous mutations I used only the former by mistake.

im3sanger commented 3 years ago

Thank you, ArashDepp. I am closing this issue now as it seems to be solved, but do not hesitate to reopen it if needed.

Best, Inigo