Closed MikeDMorgan closed 1 year ago
Be explicit about function imports - setdiff isn't defined anywhere (also, why not just use the base::diff?): https://github.com/MarioniLab/miloDE/blob/d763aa0fa6c11cbf17eb08c108c6dfe18b51b168/R/de_test_all_hoods.R#L59
base::diff
Don't use F and T as these can easily be overwritten by users, use TRUE and FALSE explicitly: https://github.com/MarioniLab/miloDE/blob/d763aa0fa6c11cbf17eb08c108c6dfe18b51b168/R/de_test_all_hoods.R#L63 https://github.com/MarioniLab/miloDE/blob/d763aa0fa6c11cbf17eb08c108c6dfe18b51b168/R/de_test_all_hoods.R#L99 https://github.com/MarioniLab/miloDE/blob/d763aa0fa6c11cbf17eb08c108c6dfe18b51b168/R/de_test_all_hoods.R#L106
F
T
TRUE
FALSE
You can define the output order of topTags, it doesn't need to be done here, or set topTags(..., sort.by='none'): https://www.rdocumentation.org/packages/edgeR/versions/3.14.0/topics/topTags https://github.com/MarioniLab/miloDE/blob/d763aa0fa6c11cbf17eb08c108c6dfe18b51b168/R/de_test_all_hoods.R#L254
topTags
topTags(..., sort.by='none')
@MikeDMorgan - setdiff is from the base package - what do you mean by 'setdiff isn't defined anywhere'?
setdiff
My bad - ignore that
done
Be explicit about function imports - setdiff isn't defined anywhere (also, why not just use the
base::diff
?): https://github.com/MarioniLab/miloDE/blob/d763aa0fa6c11cbf17eb08c108c6dfe18b51b168/R/de_test_all_hoods.R#L59Don't use
F
andT
as these can easily be overwritten by users, useTRUE
andFALSE
explicitly: https://github.com/MarioniLab/miloDE/blob/d763aa0fa6c11cbf17eb08c108c6dfe18b51b168/R/de_test_all_hoods.R#L63 https://github.com/MarioniLab/miloDE/blob/d763aa0fa6c11cbf17eb08c108c6dfe18b51b168/R/de_test_all_hoods.R#L99 https://github.com/MarioniLab/miloDE/blob/d763aa0fa6c11cbf17eb08c108c6dfe18b51b168/R/de_test_all_hoods.R#L106You can define the output order of
topTags
, it doesn't need to be done here, or settopTags(..., sort.by='none')
: https://www.rdocumentation.org/packages/edgeR/versions/3.14.0/topics/topTags https://github.com/MarioniLab/miloDE/blob/d763aa0fa6c11cbf17eb08c108c6dfe18b51b168/R/de_test_all_hoods.R#L254