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buenrostrolab / FigR

Functional Inference of Gene Regulation
https://buenrostrolab.github.io/FigR/
MIT License
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Recommend explicity qualifying namespaces #6

Closed riguyer closed 1 year ago

riguyer commented 2 years ago

Hi, I'm really enjoying using these tools to explore multiomic single-cell data. If I might make a recommendation, please consider explicitly qualifying namespaces for function calls. I've run into problems with the runGenePeakcorr() functiuon, specifically because the calls to dplyr::filter (lines 305 and 311 here) clash with the Bioconductor ensembldb package's filter function. I am able to get around this either by unloading ensembldb, which I may not always want to do, or by editing the code to explicitly name the dplyr package. Explicit namespace qualifying is recommended by the Google R Style Guide. Thanks!

vkartha commented 1 year ago

Thanks for pointing this out, definitely aware this can be annoying to debug once you realize other packages loaded may have conflicting function calls due to naming conventions. I tried my best to follow explicit function naming, but I might have missed a few cases. I will clean this up in the upcoming commit!