TreeSummarizedExperiment-accessor: TreeSummarizedExperiment-accessors

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

Description

All accessor functions that work on SingleCellExperiment should work on TreeSummarizedExperiment. Additionally, new accessors rowLinks colLinks, rowTree and colTree accessor function are available for TreeSummarizedExperiment.

Usage

rowLinks(x)

## S4 method for signature 'TreeSummarizedExperiment'
rowLinks(x)

colLinks(x)

## S4 method for signature 'TreeSummarizedExperiment'
colLinks(x)

rowTree(x)

## S4 method for signature 'TreeSummarizedExperiment'
rowTree(x)

colTree(x)

## S4 method for signature 'TreeSummarizedExperiment'
colTree(x)

## S4 method for signature 'TreeSummarizedExperiment,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 replacement method for signature 'TreeSummarizedExperiment'
rownames(x) <- value

## S4 replacement method for signature 'TreeSummarizedExperiment'
colnames(x) <- value

subsetByNode(x, rowNode, colNode)

## S4 method for signature 'TreeSummarizedExperiment'
subsetByNode(x, rowNode, colNode)

Arguments

x	A TreeSummarizedExperiment object
i, j	The row, column index to subset x. The arguments of the subset function []
...	The argument from the subset function []
drop	A logical value, TRUE or FALSE. The argument from the subset function []
value	the new rownames or colnames as a character value. See BiocGenerics.
rowNode	A vector of nodes that are used to subset rows. One could use the node number, the node label or the node alias to specify nodes, but not a mixture of them.
colNode	A vector of nodes that are used to subset columns. One could use the node number, the node label or the node alias to specify nodes, but not a mixture of them.

Value

Elements from TreeSummarizedExperiment.

Author(s)

Ruizhu HUANG

See Also

TreeSummarizedExperiment SingleCellExperiment

Examples

# the assay table
set.seed(1)
y <- matrix(rnbinom(300,size=1,mu=10),nrow=10)
colnames(y) <- paste(rep(LETTERS[1:3], each = 10), rep(1:10,3), sep = "_")
rownames(y) <- tinyTree$tip.label

# the row data
rowInf <- DataFrame(var1 = sample(letters[1:3], 10, replace = TRUE),
                    var2 = sample(c(TRUE, FALSE), 10, replace = TRUE))
# the column data
colInf <- DataFrame(gg = factor(sample(1:3, 30, replace = TRUE)),
                    group = rep(LETTERS[1:3], each = 10))

# the tree structure on the rows of assay tables
data("tinyTree")

# the tree structure on the columns of assay tables
sampTree <- ape::rtree(30)
sampTree$tip.label <- colnames(y)

# create the TreeSummarizedExperiment object
toy_tse <- TreeSummarizedExperiment(assays = list(y),
                                    rowData = rowInf,
                                    colData = colInf,
                                    rowTree = tinyTree,
                                    colTree = sampTree)

## extract the rowData
(rowD <- rowData(x = toy_tse))

## extract the colData
(colD <- colData(x = toy_tse))

## extract the linkData
# on rows
(rowL <- rowLinks(x = toy_tse))
# on columns
(colL <- colLinks(x = toy_tse))

 ## extract the treeData
# on rows
(rowT <- rowTree(x = toy_tse))
# on columns
(colT <- colTree(x = toy_tse))

TreeSummarizedExperiment documentation built on Dec. 8, 2020, 2 a.m.