The difference between major_copy_number and parental_copy_number

[王浩]

Hi Andrew, 

Could you please explain in detail the difference between major_copy_number and parental_copy_number in the parameter -- prior?

Best regards,

Hao Wang

[Andrew]

Hi Hao,

- major_copy_number considers considers more possible states, essentially allowing the number of mutant alleles to from 1 to the major copy number value

- parent_copy_number considers fewer states allowing the number of mutant alleles to be either the major or minor copy number values

In general I suggest using major_copy_number because it is vaguer prior and less likely to be incorrect.

Best wishes,

Andy

[王浩]

Dear professor Andrew Roth

Thanks for the prompt response Andy! 

I have another question. I am a new user for PyClone, But the URL " https://bitbucket.org/aroth85/pyclone/wiki/Usage  " you provided before is no longer accessible. Is there any way to learn pyclone in more detail?

Best wishes,

Hao Wang  



[Andrew]

Hi Hao,

Unfortunately the BitBucket wiki got lost when mercurial got deactivated. Details on running the software are here now https://github.com/Roth-Lab/pyclone, though a bit sparser than before. The details on the theory is all in the supplement of the Nature Methods paper.

Cheers,

Andy

[王浩]

Dear professor Andrew Roth

Thanks for your reply! 

I encountered a new problem today ! I tried to explore the use of the parameter "config_extras_file", but an error occurred when I set the "samples" attribute in the yaml file. I want to know how to set the parameter "--samples" in the "yaml" file, and then pass "--config_extras_file" to use! Would you please give me an example, thank you!

Best wishes,

Hao Wang