TASK: Preserve sample and chromosome names

pneuvial / c3co

Inferring cancer cell clonality from copy-number data

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TASK: Preserve sample and chromosome names #35

Open HenrikBengtsson opened 6 years ago

HenrikBengtsson commented 6 years ago

We should try to preserve sample and chromosome names throughout the pipeline, if they exist in the input data.

I've just added the C3coSegmentation class for objects returned by segmentData(), e.g.

> print(seg)
C3coSegmentation: 
 Method: jointseg::jointSeg
 Number samples: 3
 Number chromosomes: 24
 Number segments: 400
 Dimensions: [3] 'Y1', 'Y2', 'Y'

Ideally we could also report (and subset on) sample and chromosome names, e.g.

> print(seg)
C3coSegmentation: 
 Method: jointseg::jointSeg
 Samples: [3] 'SampleA', 'SampleB', 'SampleC'
 Chromosomes: [24] '1', '2', ..., 'Y'
 Number segments: 400
 Dimensions: [3] 'Y1', 'Y2', 'Y'

This will also be handy when plotting c3co results.

HenrikBengtsson commented 6 years ago

I've updated such that:

loadPSCBSdata(x) preserves names(x), and if that is not set, the sampleName():s of the PSCBS objects.
segmentData(x) preserves names(x) in colnames() of the Y, Y1, and Y2 elements.
c3co() already preserves the sample names as rownames() (because transposed) of the different internal estimates.

HenrikBengtsson commented 5 years ago

Known remaining tasks:

[ ] getToyData() to label samples Sample1, Sample2, ...
[ ] Add chromosomeNames() for C3coSegmentation
[ ] Update print() for C3coSegmentation to use chromosomeNames()
[ ] Plot functions to display sample names
[ ] Plot functions to display chromosome names(?)
[ ] positiveFusedLasso() to preserve sample names:
- [ ] names(mu[[m]])
- [ ] rownames(Y[[m]])
- [ ] rownames(Yhat[[m]])
[ ] ...?