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UCLouvain-CBIO / scp

Single cell proteomics data processing
https://uclouvain-cbio.github.io/scp/index.html
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Missing values vignette #40

Open lgatto opened 1 year ago

lgatto commented 1 year ago

I have done some edits.

In addition, here are some comments:

  1. Explain why counting during aggregation, if there's any reason.
  2. Wouldn't a function to create the peptide identification matrix be useful? I think this would then also address the previous point.
  3. I think a function that computes the metrics would be useful too. It could either take a feature identification matrix as input, or directly an assay.
  4. A function to calculate the cumulative sensitivity curve in the package would be welcome. I think that the code is too complex to be written as this, 'on-the-fly'.
  5. The prediction functions should also be added to the package.
cvanderaa commented 1 year ago

Good points!

For comments 1 and 2, a function to generate the identification table would be useful. Now that I think about it, this is easily implemented by providing an aggregation function that returns 1 if any row (feature) for a column (sample) is not zero and returns 0 otherwise. Do you prefer we keep the aggregation step and the step that generates the identification table separated?

For comments 3 to 5, I fully agree that dedicated functions would come handy and make the vignette much cleaner. I was not yet able to take the time to think about the implementation. I'll keep you updated here.

cvanderaa commented 1 year ago

The points are solve by #41, but I still need to write some unit tests.