TreeSummarizedExperiment-constructor: Construct a TreeSummarizedExperiment object

Description Usage Arguments Details Value Author(s) See Also Examples

Description

TreeSummarizedExperiment constructs a TreeSummarizedExperiment object.

Usage

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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.

More details about the LinkDataFrame in the rowData or colData.

Value

a TreeSummarizedExperiment object

Author(s)

Ruizhu HUANG

See Also

TreeSummarizedExperiment TreeSummarizedExperiment-accessor SingleCellExperiment

Examples

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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 16, 2021, 2:11 p.m.