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Question: Classes and methods for working with segmented copy number data
1
gravatar for Sean Davis
18 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:

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.

ADD COMMENTlink modified 10 months ago by Marcel Ramos ♦♦ 90 • written 18 months ago by Sean Davis21k
2
gravatar for Marcel Ramos
18 months ago by
Marcel Ramos ♦♦ 90
United States
Marcel Ramos ♦♦ 90 wrote:

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 

ADD COMMENTlink written 18 months ago by Marcel Ramos ♦♦ 90
2
gravatar for Marcel Ramos
10 months ago by
Marcel Ramos ♦♦ 90
United States
Marcel Ramos ♦♦ 90 wrote:

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

ADD COMMENTlink written 10 months ago by Marcel Ramos ♦♦ 90

Update: RaggedExperiment is now in Bioconductor devel!

ADD REPLYlink modified 10 months ago • written 10 months ago by Marcel Ramos ♦♦ 90
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