Metaphlan & counts

[antagomir]

The metaphlan pipeline is providing only the relative abundance assay, and not counts. This is sometimes inconvenient for various standard metagenomic analysis methods and workflows that expect counts.

The curatedMetagenomicData resource has solved this as follows (see ?curatedMetagenomicData::curatedMetagenomicData)

Finally, if a ‘relative_abundance’ resource is requested and ‘counts = TRUE’, relative abundance proportions will be multiplied by read depth and rounded to the nearest integer.

It could be useful if mia provided such functionality, at least for metaphlan import and potentially more broadly. Then the users could always have access to "counts" assay and more readily use standard tools.