Cna vignette

[alrein-05]

What changes are proposed in this pull request?
-Added basic definitions and information about copy number analysis including how to obtain the two forms of copy number data from cBioPortal, and a basic outline of creating a copy number heatmap using seg.means data

If there is an GitHub issue associated with this pull request, please provide link.

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[karissawhiting]

@alrein-05 This looks really good! Thanks very much for adding :)

I think next steps include:

• Adding an Introduction section explaining when/ why someone would want to analyze copy number data and stating the aim of the vignette (do you have a reference paper we can add with an example of a good CNA analysis? Doesn't have to be MSK). This could be combined with your current 'What are copy number alterations' section.
• Expanding outline into more descriptive sections in the style of the other vignette: https://mskcc-epi-bio.github.io/gnomeR/articles/data-processing-vignette.html
• Adding some code and an example working through seg data for users to follow along in the vignette. For now we can use the example seg file in the package: gnomeR::seg
• Are there any additional types of analysis you do on this data after you create heatmaps? Hannah and I can share the workflow outline Caroline gave us and we can add from there as well.

Do you have time/interest to continue with these updates? We'd love your continued input but if not, no worries. @hfuchs5 and I can take over.

Thanks again for your great work!

[karissawhiting]

This PR was combined with PR #297