Rename transformCounts to transformAssay

[antagomir]

The transformCounts is somewhat misleading name bc this function allows transformation for any assay (not just counts assay).

Let us change the name to transformAssay and deprecate transformCounts.

Remember to update

• unit tests
• manpage
• vignettes
• oma
• miaViz
• miaSim
• miaTime

[antagomir]

Merged - remember to update the other resources as well.

It might be easiest to do this after we first updated this mia version to Bioconductor devel; we have many updates recently and it is good to bring them there for further testing (if not done already) ping @TuomasBorman when the time allows?

[TuomasBorman]

Bioc devel should be updated in couple of days

[antagomir]

Still on thing to fix.

Load example data first:

library(mia)
data(GlobalPatterns, package="mia")

Then running transformCounts(GlobalPatterns) gives:

Error in transformCounts(GlobalPatterns) : could not find function "transformCounts"

-> This means that the transformCounts has not been deprecated properly. The old function name should continue working during some transition period. Looking at the code, line 236 onwards it seems that this actually should throw a warning but work. Investigate why it throws an error instead or warning. I also think that line 237 should have .Deprecate message instead of warning?

[antagomir]

@ake123 can you check?

[TuomasBorman]

This is also done @ake123 ? And this and other functions are deprecated properly? (Old ones are still available but function gives deprecation message)

[ake123]

it was done!

[antagomir]

can you close issues that are ready? after checking that deprecations are OK in mia, and function names corrected also in miaViz, miaTime, miaSim, OMA (if used in those)

[ake123]

All fixed!