treeSummarizedExperiment-class: An S4 class treeSummarizedExperiment

In markrobinsonuzh/treeAGG: Tree Aggregation

Description

The class treeSummarizedExperiment is an extension class of standard SummarizedExperiment-class class. It has six slots. Four of them are traditional slots from SummarizedExperiment-class class: assays, rowData colData and metadata. The other two slots are linkData and treeData. The class treeSummarizedExperiment is designed to store rectangular data for entities (e.g., microbes or cell types) (assays), information about the hiearchical structure of entities (treeData), and information about the mapping between the rows of the rectangular data and the nodes of the tree (linkData).

Slots

linkData

A DataFrame-class object. It gives map information between the rows of rectangular data and the nodes of tree.

• nodeLab The node labels on the tree.

• nodeLab_alias An alias of column nodeLab. It is created only when there are missing value or duplicated value in column nodeLab. A prefix "Node_" and "Leaf_" is added to the node number (column nodeNum) for the internal nodes and the leaf nodes, respectively.

• nodeNum The node numbers on the tree.

• isLeaf This indicates whether a node is a leaf node.

• rowID The row number in assays.

treeData

A phylo object. It gives information about the hiearchical structure of the entities.

...

See SummarizedExperiment-class for more details about the slots inherited from SummarizedExperiment class.

Constructor

See treeSummarizedExperiment-constructor for constructor functions.

Accessor

See treeSummarizedExperiment-accessor for accessor functions.

See Also

treeSummarizedExperiment treeSummarizedExperiment-accessor leafSummarizedExperiment SummarizedExperiment-class

markrobinsonuzh/treeAGG documentation built on May 26, 2019, 9:32 a.m.