Compare CNV profiles across many patients

[augjensen]

Can the CNAmtx.RData (I have these from previous analysis outputs) be used to regenerate the CNV heatmap and if so, is it possible to merge hundreds of samples together, something that is not possible when running the package due to memory limitations. My concern is that the CNVs are probably normalized for each sample, therefore it is not possible to compare the results between samples?

Preferably I would like to generate subclones for each patient and compare these between hundreds of patients. How would one go about trying to compare subclones/CNV profiles between hundreds of patients?