rowLinks {TreeSummarizedExperiment} | R Documentation

## TreeSummarizedExperiment-accessors

### 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))

[Package TreeSummarizedExperiment version 1.6.2 Index]