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ShixiangWang / DoAbsolute

:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package
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"Allelic" parameter error #20

Closed joonan30 closed 2 years ago

joonan30 commented 2 years ago

Hi Shixiang,

Thanks for the wonderful tool. I ran successfully with "total" parameter for the copy.num.type but when I set to "allelic", it does not work. The error message is:

> Checking result files...
-> Checked.
-> Removed previous temp review result directory.
-> Running Absolute summarize...
..............................Error in round(hscn.params[["sigma.eta"]], 3) : 
  non-numeric argument to mathematical function

Do you have any idea on this?

Best, Joon

ShixiangWang commented 2 years ago

Hi @joonan30 ,

you can check https://software.broadinstitute.org/cancer/cga/absolute_run

image

Best

joonan30 commented 2 years ago

Thanks, it was my bad. My input is not for HAPSEG so it shouldn't work.

Can I have another question? From the result, none of my samples (WES) was predicted to have "genome double" , which I assume some of samples would be. Do you think it's related to parameters or WES (or possibly no genome doubled samples) ?

Thanks!!

ShixiangWang commented 2 years ago

@joonan30 I don't know. But you can try Sequenza or Facets to check the tumor genome ploidy. If truly a WGD, a ploidy value >= 4 (or close) should be observed.

joonan30 commented 2 years ago

Thansk Shixiang, I was able to get it by facets. Many thanks for your time (and tool as well!!)

Best,