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ocbe-uio / DIscBIO

A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics
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The PPI function is writing to the user's disk #33

Closed wleoncio closed 4 years ago

wleoncio commented 4 years ago

Summary

The following lines of PPI() always write and read a file from the user's local drive:

https://github.com/ocbe-uio/DIscBIO/blob/5b2b23aa5b5dd1440e4982dd6c2435dcfabfdf55/R/PPI.R#L42-L45

DIscBIO version

1.1.0

Expected output

R functions are not supposed to write on the user's working directory unless explicitly told to.

wleoncio commented 4 years ago

This issue was discovered while handling issue #29. A fix should be issued ASAP.

wleoncio commented 4 years ago

@SystemsBiologist, repo_content is a 3D array with the following lengths:

> dim(repo_content)
[1] 5627 5449    4

When saving the results as a CSV file, only the first 5627x5449 matrix is saved (that's the default behavior of write.csv). Why are the other 3 discarded?

SystemsBiologist commented 4 years ago

Because we are only interested in the PPI data

wleoncio commented 4 years ago

Got it. We still need to replace the writing/reading with something that internally handles this, though. I imagine results <- data.frame(repo_content[, , 1]) will suffice. I'll issue a PR with that for you to review. Sorry, I had a brain fart and ended up commiting to dev straight up and forgot the PR. @SystemsBiologist, please check out the changes made on commit e2915183d094593bd51913ee7bee3d4159da99bc and let me know if they are OK.