Question: Classes and methods for working with segmented copy number data
1
2.9 years 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.

cgh copynumber • 665 views
modified 2.3 years ago by Marcel Ramos ♦♦ 360 • written 2.9 years ago by Sean Davis21k
Answer: Classes and methods for working with segmented copy number data
2
2.9 years ago by
Marcel Ramos ♦♦ 360
United States
Marcel Ramos ♦♦ 360 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

Answer: Classes and methods for working with segmented copy number data
2
2.3 years ago by
Marcel Ramos ♦♦ 360
United States
Marcel Ramos ♦♦ 360 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