There are dozens of packages for working with copy number data available in Bioconductor.  However, I don’t get the sense that there is a class that unifies the somewhat standardized “processed” output that consists of:

• sample_id
• chromosome
• start_pos
• end_pos
• copy_number

I am interested in applying something like gistic over my data, summarizing to gene, etc. Any suggestions on classes (and associated methods) would be much appreciated.

Hi Sean!

We have the `MultiAssayExperiment::RangedRaggedAssay` class that can handle all of the above.

It would require you to have a `GRangesList` object with a "score" metadata column denoting copy_number. The `GRangesList` can be created from a `DataFrame` using the `GenomicRanges::makeGRangesListFromDataFrame` and subsequently converted to RangedRaggedAssay from `MultiAssayExperiment`. 

I hope this helps and feel free to reach out for more details. We have a run-able example in the package via `example("RangedRaggedAssay")`.

Marcel 

Update: Please see the latest package submission (RaggedExperiment) for this type of data. https://github.com/Bioconductor/Contributions/issues/339 and the GitHub version of the package https://github.com/Bioconductor/RaggedExperiment/ 

Sincerely, 

Marcel