I seem to always get this warning from PureCN.R, is it anything to be concerned about?
WARN [2018-04-27 12:38:09] test.num.copy outside recommended range.
The warning just is what is says, you most likely set test.num.copy to non-default values that are not good. The defaults are fine. See the documentation for this parameter in runAbsoluteCN.
I did not set test.num.copy, and furthermore, no PureCN program shows that as an option argument.
Maybe it has another name?
Yes, there are sometimes different names for parameters in the command line tools for various reasons. They are all documented in the appendix of the Quick vignette.
If you used the command line tools, then you likely set --maxcopynumber to a high value. This specifies the range of tested integer copy numbers. The difference between two consecutive integer states becomes very small with increasing copy number. In average clinical samples, you cannot distinguish 7 from 8 copies anymore. In high quality, high purity, you maybe can, but 8 and 9 becomes pretty much impossible.
As documented, that does not mean PureCN does not accurately call amplifications with higher copy number. Everything that does not fit the tested integer numbers will be simply reported as non-integers.
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