1. Anatomy of a MPSE
MPSE S4 class. This class inherits the
SummarizedExperiment(Morgan et al. 2021) class. Here, the
assays slot is used to store the rectangular abundance matrices of features for a microbiome experimental results. The
colData slot is used to store the meta-data of sample and some results about samples in the downstream analysis. The
rowData is used to store the meta-data of features and some results about the features in the downstream analysis. Compared to the
MPSE introduces the following additional slots:
- taxatree: is a
treedata(Wang et al. 2020; Yu 2021) class contained phylo class (hierarchical structure) and tibble class (associated data) to store the taxonomy information, the tip labels of taxonomy tree are the rows of the
assays, but the internal node labels contain the differences level taxonomy of the rows of the
assays. The tibble class contains the taxonomy classification of node labels.
- otutree: is also a
treedataclass to store the phylogenetic tree (based with reference sequences) and the associated data, which its tip labels are also the rows of the assays.
- refseq: is a
XStringSet(Pagès et al. 2021) class contained reference sequences, which its names are also identical with the rows of the assays.