Tuomas Borman

Any updates on this? Should we go with generic function or specific functions for each type convertFromPhyloseq/convertToPhyloseq

It works nicely but the problem is that the package loading gives warning. This is caused because the class in generic. For example phyloseq class is not detected if phyloseq...

If you cannot find solution for this, we can also rename the existing functions and move the documentation under shared "convert" page. - makeTreeSEFromPhyloseq --> convertFromPhyloseq - makeTreeSEFromBiom --> convertFromBIOM...

This is what happens ``` > devtools::load_all() ℹ Loading mia in method for ‘convert’ with signature ‘x="dada"’: no definition for class “dada” in method for ‘convert’ with signature ‘x="phyloseq"’: no...

Any thoughts @antagomir

\+ convert() is very neat solution \- We cannot have more dependencies, we have too many already \- We cannot have notes, when package is loaded. It does not look...

https://github.com/microbiome/mia/pull/591

This is already done @RiboRings ?

> The `getDominantTaxa` parts of which are inspired from [microbiomeutilties::dominant_taxa](https://github.com/microsud/microbiomeutilities/blob/master/R/dominant_taxa.R) can be renamed as `summarizeDominantTaxa` as it returns a tibble with overview. On the other hand, `dominantTaxa` adds a column...

So, if I understood correctly 1 There should be additional R/Rmd files (`qc-functions`) for summarization functions. - `summarizeDominantTaxa` (currently `getDominantTaxa`) should be moved there - all other functions for summarization...