Extension to correlated observables
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Description
Which problem would you like to address? Please describe.
Mapping of phospho-peptides to protein phospho sites can be ambiguous, leading to correlations in the measured data. This could be captured in the noise model, but PEtab currently doesn't allow the specification of such relationships.
Describe the solution you would like
Extend the PEtab to allow the specification of correlation groups. Specific format would have to be discussed.
Describe alternatives you have considered
Alternative is probably summation of observables to avoid errors from unaccounted correlations.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No files or tests are identified in the issue. Start by reviewing the PEtab observable and noise-model specifications, then determine how correlation groups for phospho-peptide measurements should be represented. Done means the format is agreed and PEtab supports specifying and interpreting those relationships.
Written by the indexing model from the issue text.
Assessment
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100