In both marker-gene sequencing and shotgun metagenomics, we identify the data consist four components.

  1. contingency table of read counts.

  2. matrix of specimen information.

  3. matrix of taxa identifiers at several selected taxonomy levels.

  4. phylogenetic tree.

Given a data set with all four components, we create a phyloseq object and use it for the analyses. Please refer to phyloseq website to learn about the phyloseq class.