TreeSummarizedExperiment-constructor: Construct a TreeSummarizedExperiment object

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

Construct a TreeSummarizedExperiment object

Description

TreeSummarizedExperiment constructs a TreeSummarizedExperiment object.

Usage

TreeSummarizedExperiment(
  ...,
  rowTree = NULL,
  colTree = NULL,
  rowNodeLab = NULL,
  colNodeLab = NULL,
  referenceSeq = NULL
)

Arguments

...	Arguments passed to the SummarizedExperiment constructor to fill the slots of the base class.
rowTree	A phylo object that provides hiearchical information of rows of assay tables.
colTree	A phylo object that provides hiearchical information of columns of assay tables.
rowNodeLab	A character string. It provides the labels of nodes that the rows of assays tables corresponding to. If NULL (default), the row names of the assays tables are used.
colNodeLab	A character string. It provides the labels of nodes that the columns of assays tables corresponding to. If NULL (default), the column names of the assays tables are used.
referenceSeq	A DNAStringSet/DNAStringSetList object or some object coercible to a DNAStringSet/DNAStringSetList object. See DNAStringSet for more details.

Details

The output TreeSummarizedExperiment object has very similar structure as the SingleCellExperiment. The differences are summarized be as below.

• rowTree A slot exists in TreeSummarizedExperiment but not in SingleCellExperiment. It stores the tree structure(s) that provide(s) hierarchical information of assays rows or columns or both.

• rowData If a phylo object is available in the slot treeData to provide the hiearchical information about the rows of the assays table, the rowData would be a LinkDataFrame-class instead of DataFrame. The data on the right side of the vertical line provides the link information between the assays rows and the tree phylo object, and could be accessed via linkData; The data on the left side is the original rowData like SingleCellExperiment object.

• colData Similar to the explanaition for rowData as above.

More details about the LinkDataFrame in the rowData or colData.

• nodeLab The labels of nodes on the tree.

• nodeLab\_alias The alias of node labels on the tree.

• nodeNum The numbers of nodes on the tree.

• isLeaf It indicates whether the node is a leaf node or internal node.

Value

a TreeSummarizedExperiment object

Author(s)

Ruizhu HUANG

See Also

TreeSummarizedExperiment TreeSummarizedExperiment-accessor SingleCellExperiment

Examples

data("tinyTree")

# the count table
count <- matrix(rpois(100, 50), nrow = 10)
rownames(count) <- c(tinyTree$tip.label)
colnames(count) <- paste("C_", 1:10, sep = "_")

# The sample information
sampC <- data.frame(condition = rep(c("control", "trt"), each = 5),
                    gender = sample(x = 1:2, size = 10, replace = TRUE))
rownames(sampC) <- colnames(count)

# build a TreeSummarizedExperiment object
tse <- TreeSummarizedExperiment(assays = list(count),
                                colData = sampC,
                                rowTree = tinyTree)

fionarhuang/TreeSummarizedExperiment documentation built on June 11, 2025, 9:42 a.m.