leafSummarizedExperiment-class: An S4 class leafSummarizedExperiment
In markrobinsonuzh/treeAGG: Tree Aggregation

Description Details Constructor Accessor Author(s) See Also

The class leafSummarizedExperiment is an extension class of standard SummarizedExperiment-class class. It is designed to store rectangular data like a matrix for entities (e.g., microbes or cell types), and the information of the hiearchical structure of entities. The annotations on the rows and columns of the rectangular data are strored in rowData and colData, respectively. Each row of the rectangular data could be mapped to a leaf node of the tree via the rownames of rowData or a column named as nodeLab in rowData. For example, the abundance count of microbes collected from different samples could be stored in the assays and the phylogenetic tree of the microbes in the metadata. Each row of matrix-like data in assays represents one microbial specie that could be mapped to a leaf node of the phylogenetic tree. The link between the row and the node could be given via a column (nodeLab), or the rownames of rowData. Each column of the matrix-like data is a sample. The sample information is given in the colData. The class leafSummarizedExperiment has four slots assays, rowData colData and metadata as the SummarizedExperiment-class class. More details about these four slots could be found in SummarizedExperiment-class.

The leafSummarizedExperiment class has more restrictions in data structure than the SummarizedExperiment class. In leafSummarizedExperiment class, it's required that

A phylo object is stored in metadata and named as tree. The phylo object has a unique label for each leaf node.
Each rows of matrix-like data in assays could be mapped to a leaf node of the tree. The label of leaf node is provided as the column nodeLab in rowData, or as the rownames of rowData or assays. If both provided, the information in column nodeLab is used.