Hello,

I am currently downloading relative abundance datasets using the script below. While the download completes successfully, all the features in the output are at the species level. However, I am also interested in obtaining relative abundances for higher taxonomic levels, such as genera and families.

In my previous work with MetaPhlAn outputs, the results typically included higher taxonomic units, but in this case, I am only receiving species-level data.

Does anyone know why this might be happening, or how I can modify the process to include higher taxonomic levels?

This is the format in which I would prefer to have the taxonomic units:

k__Bacteria k__Bacteria|p__Actinobacteria k__Bacteria|p__Actinobacteria|c__Actinobacteria k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum_massiliense

relative_abundance_data <- curatedMetagenomicData(".relative_abundance", dryrun = FALSE)
View(relative_abundance_data)

saveRDS(relative_abundance_data, file = "relative_abundance_data.rds")
print("ABUNDANCE DATA SAVED")

I'm sorry I missed the first post! Yes, it is easy to agglomerate ranks in curatedMetagenomicData datasets. See the example in the vignette section Agglomerate Ranks - you just use the mia::splitByRanks() function.