TreeSummarizedExperiment-class {TreeSummarizedExperiment} | R Documentation

## An S4 class TreeSummarizedExperiment

### 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`

[Package TreeSummarizedExperiment version 2.2.0 Index]