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rformassspectrometry / QFeatures

Quantitative features for mass spectrometry data
https://RforMassSpectrometry.github.io/QFeatures/
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Implement a c method - solves Issue#166 #169

Closed cvanderaa closed 2 years ago

cvanderaa commented 2 years ago

(Please first merge PR #170)

In this PR I implement the c(),QFeatures method for combining QFeatures objects. I took a few liberties that require your attention:

  1. I moved away from the c(),MultiAssayExperiment because it does not correctly handle the merging of colData. In this implementation, I make sure that when 2 QFeatures object have conflicting colData information, an error is thrown. In the other cases, the colData is merged as for addAssay(), taking into account the addition of new samples.
  2. I only allow user to provide QFeatures objects. If they provide a list or an object that inherits from List or SummarizedExperiments, the method throws an error and suggest addAssay() instead. If they provide something else than those or a QFeatures object, the objects are converted to a QFeatures obbject.
  3. I allowed QFeatures objects to be combined with MultiAssayExperiment objects. This required to implement a coerce method from MultiAssayExperiment to QFeatures, because the generic implementation leads to an invalid (empty) assayLinks slot.
  4. Beside the c(),QFeatures method, I implement the nrows() and ncols() methods. They would be handy next to dims().
cvanderaa commented 2 years ago

I reverted the version bump when merging the current master (so it's still 1.7.2). Let me know if I need to bump the version.

lgatto commented 2 years ago

@cvanderaa - could you confirm that this PR can be merged.

cvanderaa commented 2 years ago

PR is ready for merging.