Detecting annotation discrepancies

bartongroup / RATS

Relative Abundance of Transcripts: An R package for the detection of Differential Transcript isoform Usage.

MIT License

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Detecting annotation discrepancies #52

Closed fruce-ki closed 6 years ago

fruce-ki commented 6 years ago

In response to #49 .

Although users are explicitly instructed not to mix up annotations, it seems prudent to have RATs at least produce some warnings.

This can be done

at the end of the run, leveraging NA in certain fields
or at the beginning of the run as a thorough pre-check of ID sets across the inputs and lead to aborting the run, potentially with a force option to override the abort.

fruce-ki commented 6 years ago

I've decided it is best to encourage good practices instead of trying to clean up after bad ones. Therefore, any mismatch of transcript IDs between the annotation and the quantifications will now result in aborting the run.

I remain unsure still whether to allow an explicit override. It would certainly simplify updating the unittests, as the testing dataset explicitly contains cases with inconsistent annotation that make the new abort condition cause all the tests to fail.