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Question: Classes and methods for working with segmented copy number data
1
gravatar for Sean Davis
13 months ago by
Sean Davis20k
United States
Sean Davis20k 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 5 months ago by Marcel Ramos ♦♦ 60 • written 13 months ago by Sean Davis20k
2
gravatar for Marcel Ramos
13 months ago by
Marcel Ramos ♦♦ 60
United States
Marcel Ramos ♦♦ 60 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 13 months ago by Marcel Ramos ♦♦ 60
2
gravatar for Marcel Ramos
5 months ago by
Marcel Ramos ♦♦ 60
United States
Marcel Ramos ♦♦ 60 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 5 months ago by Marcel Ramos ♦♦ 60

Update: RaggedExperiment is now in Bioconductor devel!

ADD REPLYlink modified 5 months ago • written 5 months ago by Marcel Ramos ♦♦ 60
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