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Bioconductor / LoomExperiment

A package to read, write, and manipulate loom files using LoomExperiments. Uses the loom file format from the Linnarson Lab. https://linnarssonlab.org/loompy/
https://www.bioconductor.org/packages/LoomExperiment
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Fixes to export and import consistency, closes #10 #11

Closed LiNk-NY closed 4 years ago

LiNk-NY commented 4 years ago

Hi Daniel, @dvantwisk

Please review the changes in this PR. In reference to #10, I've made sure that there are consistent colnames and rownames in reducedDims, and factors as they were in colData before exporting (this part of the code could be improved so that all types are the same before and after exporting / importing). I've also addressed the issue in the build report by modifying the tests so that they do not check the attributes.

I also had an issue with the transposition section so I had to develop a helper function to make sure assays are being transposed when they should be and the conditional statements evaluate to logical.

Best, Marcel

LiNk-NY commented 4 years ago

This looks good to me. I've tested locally and it passes the tests. @dvantwisk