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saezlab / cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
https://saezlab.github.io/cosmosR/
GNU General Public License v3.0
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reverted vapply to sapply #11

Closed adugourd closed 3 years ago

adugourd commented 3 years ago

vapply leads to crash when using a real dataset. I reverted to sapply and it works.

katharinazirngibl commented 3 years ago

Yes, indeed. The problem in real examples is that you actually have genes that are missing, hence the return of the apply function is a NA and not a character. Let's revert vapply back to sapply for now. If we want to keep vapply in future we could for example make the return of the function a boolean variable, which in a second step is used for filtering the pkn sources and targets.