Prevent failure of R script in case of single RNA sample in a 'cohort' #477
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iainrb
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Oct 25, 2024
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Code change seems reasonable, but it's resulted in some checksum failures in our unit tests. It may or may not be OK to update the checksums and proceed -- we'll investigate next week and get back to you. A few other things:
- Our procedure is not to merge directly to the
mainbranch. Instead, we have a release branch (currentlyrelease-1.7.7) which is merged tomainjust before a new release is tagged, and after internal testing and validation. I have changed the target branch torelease-1.7.7. - Any Djerba PR should include a one-line description in the
Unreleasedsection inCHANGELOG.md. - To support more collaborative development, we will look at making our tests more portable and documenting on ReadTheDocs.
Thanks and have a good weekend! 😃
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Would like to compare a single RNA sample against TCGA using Djerba, which means that the study cohort has a size of one.
Normally this should not be an issue, but R has a very annoying 'feature' where data frames with a single column are automatically converted to vectors. This breaks the find_expression.R evaluation logic, but is easily mitigated in this pull request by adding the drop=FALSE argument in three places where the study cohort data frame is sliced up in the code.