RFE: Allow feeding the models back into the QDNAseq object they were generated from

tgac-vumc / ACE

Absolute Copy Number Estimation using low-coverage whole genome sequencing data

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RFE: Allow feeding the models back into the QDNAseq object they were generated from #2

Closed lbeltrame closed 1 year ago

lbeltrame commented 4 years ago

Hello,

I think it would be worthwhile to be able to feed the fitted models (once the likely fit has been chosen by the user) for a sample group back in the segmented assayDataElement of the QDNAseq object.

The rationale is that some additional analysis tools make use of QDNAseqCopyNumbers objects, and they would benefit by ACE's modeling (I have a few problematic samples where the modeling done by ACE improves the situation). Currently this is not possible unless done manually.

jpoell commented 1 year ago

Yes that is a good point! I would have to brush up on my S4 object programming for this, and I will not have time for this in the foreseeable future. Sounds like a very nice bioinformatics student project!