TreeSummarizedExperiment-class: An S4 class TreeSummarizedExperiment

In fionarhuang/TreeSummarizedExperiment: TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

Description

The class TreeSummarizedExperiment is an extension class of standard SingleCellExperiment class. It has four more slots that are not in SingleCellExperiment class: rowTree, rowLinks colTree and colLinks. The hierarchical information of rows (columns) is stored in rowTree (colTree) and the link between the rows (columns) of assays tables and nodes of the tree is given in rowLinks (colLinks).

Details

The class TreeSummarizedExperiment is designed to store rectangular data for entities (e.g., microbes or cell types) (assays), information about the hiearchical structure (rowTree on rows; colTree on columns), and the mapping information between the tree nodes and the rows or the columns of the rectangular data. Users could provide the hiearchical structure of the rows, columns or both) of the assays tables, and the link data will be automatically generated in rowLinks, colData or both, respectively. It's required that the object in rowLinks or colLinks has the LinkDataFrame class. Please see the page LinkDataFrame for more details.

Slots

rowTree

A phylo object or NULL. It gives information about the hiearchical structure of rows of assays tables.

colTree

A phylo object or NULL. It gives information about the hiearchical structure of columns of assays tables.

rowLinks

A LinkDataFrame. It gives information about the link between the nodes of the rowTree and the rows of assays tables.

colLinks

A LinkDataFrame. It gives information about the link between the nodes of the colTree and the columns of assays tables.

referenceSeq

A DNAStringSet/DNAStringSetList object or some object coercible to a DNAStringSet/DNAStringSetList object. See DNAStringSet for more details.

...

Other slots from SingleCellExperiment

Constructor

See TreeSummarizedExperiment-constructor for constructor functions.

Accessor

See TreeSummarizedExperiment-accessor for accessor functions.

See Also

TreeSummarizedExperiment TreeSummarizedExperiment-accessor SingleCellExperiment

fionarhuang/TreeSummarizedExperiment documentation built on Aug. 18, 2021, 12:15 p.m.