Convert a phyloseq object to an agglomerated dataframe.

Source: R/metaglomr.R

Convert a phyloseq object to an agglomerated dataframe.

phyloseq_to_agglomerated(ps, sample_col, otu_col = "otu_id",
  count_col = "count")

Arguments

ps

a phyloseq object
sample_col

the sample_data() column corresponding to rownames(otu_table()), as a string
otu_col

the desired name of the otu id column
count_col

the desired name of the count column