Exploration of Data in Phyloseq - meyermicrobiolab/Meyer_Lab_Resources GitHub Wiki

If you have identified sequence variants (in place of OTUs) with dada2, fixed the taxonomy table & matching otu table, then creating a phyloseq object that combines your cleaned taxonomy table, otu table, and metadata file then you can use these commands for getting information from your phyloseq object.

  • how many taxa (OTUs/Sequence Variants)

    • ntaxa(ps)
    • nsamples(ps)

  • look at how many phyla, etc

    • get_taxa_unique(ps, "Phylum")
    • get_taxa_unique(ps, "Order")

  • tutorial with additional preprocessing options.

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