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ocbe-uio / DIscBIO

A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics
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Replace call to boot() from Jaccard() #26

Closed wleoncio closed 12 months ago

wleoncio commented 3 years ago

DIscBIO contains the boot package as a dependency just for the purpose of using the boot() function inside Jaccard() (see here). If this were to be replaced by an in-house solution, there would be one fewer dependency for DIscBIO (which is currently depending on 21 non-default packages; this generates a NOTE from devtools::check()).

wleoncio commented 3 years ago

Should be simple enough, given that boot::boot just seems to be performing simple bootstrapping. The trickier part might be replicating the summary statistics, but even these are fixed, which makes it easier to code.

FWIW, the boot package's license is "unlimited" (source), so reusing the code itself might be straightforward.

wleoncio commented 3 years ago

Since commit 13455a930af502429884592477d6f558a6a4b955 eliminated the need for the readr package, the devtools check no longer issues a "lots of dependencies" note. In this case, it might be better to leave the boot dependency, as the additional code might offset the time saved by having one fewer dependency.

In any case, perhaps a simple copy-pasting of the original code could be used as a test to see if it checks faster than having the extra dependency. In the end, check time is arguably the biggest issue to be tackled here.