Request: Custom destination directories

[jfiksel]

It would be great if the user could have an option to supply the full output directory for both CopywriteR and for plotCNA. For example, if I have whole exome data and targeted data in the same project, it would be great if I could supply the two different output directories as wes_CNAprofiles and targeted_CNAprofiles. Right now I would have to make different directories for each, and then the CNAprofiles would get saved within those directories to avoid having each CNAprofiles directory being overwritten, creating an unnecessary extra directory layer.

I would also like to supply the full destination directory for plotting--in my current workflow I would like to save the CNAprofiles directory within a "data" directory and then resulting plots in a "visualizations" directory, but right now the plots go directly within the CNAprofiles directory.

[thomasKuilman]

Thanks for your input and this sounds like a good idea. BTW, it is not possible to overwrite another folder called CNAprofiles; you would get an error message. Nevertheless, I think this would be added value to the package and we will try to include this in the next release.