altExp support for meltAssay

[antagomir]

It is not possible to choose altExp for meltAssay currently.

One can however call meltAssay(altExp(tse, ...)) to do this for any altExp. Perhaps this is enough and there is no need to complicate the function?

An example could be added on the manpage, however as there have been questions about it.

[antagomir]

altExp mechanism seems to work routinely also in transformCounts even though it is not defined in that function (i.e. it just works because the function implementation knows how to pass this argument further and make the selection; see transformCounts source code for an example).

library(mia)
data(GlobalPatterns)
tse <- GlobalPatterns
altExps(tse) <- splitByRanks(tse)
transformCounts(tse, assay.type="counts", method="relabundance", altexp="Genus")

For consistency let us make sure it works this way also for meltAssay.

Importantly, it should be (?) possible to add this implicitly by doing similar programming than in transformCounts, instead of explicitly declaring altexp as a function argument. Inspect the transformCounts source code on how to do this.

[antagomir]

@ake123 I suggest you try, ask @TuomasBorman if you bump into problems.

[ake123]

This is solved!