R code for cn.mops -- if a chromosome does not have CNV ?
Entering edit mode
Bogdan ▴ 670
Last seen 8 months ago
Palo Alto, CA, USA

Dear Gunter,

please if I may add another 1-2 questions : after running cn.MOPS per chromosome on a PBS computer cluster, sometimes, in the output it says :

"No CNVs detected. Try changing "normalization", "priorImpact" or "thresholds".
Error in calcIntegerCopyNumbers(ref_analysis_norm0) :
  No CNV regions in result object. Rerun cn.mops with different parameters!
Calls: calcIntegerCopyNumbers -> calcIntegerCopyNumbers"

and of course, that is fine, as we do not aim to identify CNV on each chromosome ;) However, please could you advise :

-- is there a way to print a message when there are no detected CNV instead of receiving the message "Error in calcIntegerCopyNumbers(ref_analysis_norm0) : " , as it would help our pipeline

-- in the message it says "Try changing "normalization", "priorImpact" or "thresholds".". Shall we change any of these parameters though ?

thanks a lot !





cn.mops referencecn.mops • 1.2k views
Entering edit mode
Last seen 3.4 years ago

Hello again,

And apologies, again, I had not seen your message until now. I see that the error is problematic for your pipeline  - you can try to catch the error using "try()". However, I will change the behaviour from "error" to "warning" in the next version of cn.mops.

You don't need to change your parameters, if you have already adjusted them and they perform well.




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