list_subset_ASVs: Returns a vector of ASVs belonging to groups at a taxonomic...
In simeross/CuPhyR: Custom Functions for Microbiome Analysis with Phyloseq

A function to list ASVs belonging to a set of taxonomic terms

1	list_subset_ASVs(physeq = ps, subv = c("e"), taxlvlsub = "Kingdom")

`physeq`	a phyloseq object to extract ASVs/OTUs ('tax_names') from
`subv`	a character vector of taxonomic terms at the level of interest
`taxlvlsub`	a character string containing a taxonomic level present in the database

a character vector of ASVs

Simeon Rossmann

1 2	phyt_ASVs <- list_subset_ASVs(physeq = ps, subv = c("Phytophthora","Phytopythium"), taxlvlsub="Genus") ps_phyt <- phyloseq::prune_taxa(phyt_ASVs, ps)