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waldronlab / bugsigdbr

R-side access to published microbial signatures from BugSigDB
https://bioconductor.org/packages/bugsigdbr
GNU General Public License v3.0
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Improve formatting #16

Closed jwokaty closed 3 years ago

jwokaty commented 3 years ago

I addressed the main points of BiocCheck and also tried to improve the formatting. I also bumped the version. Closes #15 .

lgeistlinger commented 3 years ago

I think that looks great. Only hiccup seems to be the example of writeGMT which causes the checks to fail.

I think you'll need:

bsdb <- importBugSigDB()
sigs <- getSignatures(bsdb)
writeGMT(sigs, file = "signatures.gmt")
file.remove("signatures.gmt")

in the example section of writeGMT for this to work.