Add real data vignette and data object

[lwaldron]

Real data sources to use:

1. Mutations from the AWS S3 MultiAssayExperiment for ACC
2. ABSOLUTE copy number calls for ACC (Ludwig)

Nice examples:

• creating a matrix of samples x genes, with 1 if there is a non-silent mutation in that gene.
• ditto for chip-seq peaks, open chromatin regions, e.g. from AnnotationHub
• ABSOLUTE analysis example from Ludwig
• association between copy number ranges or mutations and a colData column

[LiNk-NY]

@lwaldron, It looks like there are very few labeled mutations in the data:

> mut <- acc[["Mutations"]]
> sum(rowSums(!is.na(assay(mut, "Variant_Classification"))) > 1L)
[1] 0

With a cutoff of 1 mutation per row, we don't get any rows.

[lgeistlinger]

Depending on how much further you want to go down that road, I'm just noting here that our new CNVRanger package contains several real data examples building on RaggedExperiment.

In particular, the TCGA GBM example in Vignette, Section 5.2 (https://github.com/waldronlab/CNVRanger/blob/a5ed34d7026c6f7abccbf7288aea5fe8c73e84ff/vignettes/CNVRanger.Rmd#L423) might be a nice illustrative example.

One solution here could thus be just simply referring to CNVRanger / the respective vignette section.