Rename splitByRanks to agglomerateByRanks and add new option as.list

microbiome / mia

Microbiome analysis

https://microbiome.github.io/mia/

Artistic License 2.0

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Closed thpralas closed 1 month ago

thpralas commented 2 months ago

This PR renames splitByRanks to agglomerateByRanks and add a new argument as.list.

If as.list = TRUE : The SimpleList of agglomerated SummarizedExperiment objects is returned by agglomerateByRanks
If as.list = FALSE : The SimpleList of SummarizedExperiment objects is added to altExps of the SummarizedExperiment passed as a parameter

TuomasBorman commented 1 month ago

To summarize:

Leave splitByRanks as alias. (just empty function calling agglomerateByRanks)
In SE method, add TreeSE conversion if the class is SE. (Give warning about the conversion)
Add SCE/TreeSE specific functionality to SCE method (TreeSE is SCE). Then call SE method.
TreeSE method is just calling SCE method.