Accessor method for rowLinks from subsets in ExperimentSubset objects

Get rowLinks from a subset: the links of its rows to the nodes of the tree that subsetRowTree returns.

Usage

subsetRowLinks(x, subsetName, parentRowLinkData = TRUE)

# S4 method for class 'SubsetTreeSummarizedExperiment'
subsetRowLinks(x, subsetName, parentRowLinkData = TRUE)

Arguments

x

ExperimentSubset Input ExperimentSubset object.

subsetName

character(1) Name of the subset to get rowLinks from.

parentRowLinkData

logical(1) If TRUE (the default), a subset without a row tree of its own, or one it was made from, gets the links to the main object's row tree. If FALSE, it gets only links to a row tree stored by the subset or one it was made from, and NULL if there is none.

Value

The rowLinks of the subset's rows, with the subset's rownames, or NULL.

Examples

# a small TreeSummarizedExperiment with a tree on both rows and columns
data("tinyTree", package = "TreeSummarizedExperiment")
counts <- matrix(1:100, nrow = 10)
# name rows and columns after the tips of the tree
rownames(counts) <- tinyTree$tip.label
colnames(counts) <- tinyTree$tip.label
tse <- TreeSummarizedExperiment(assays = list(counts = counts),
                                rowTree = tinyTree, colTree = tinyTree)
es <- ExperimentSubset(tse)
es <- createSubset(es, "subset1", rows = 1:5, cols = 1:5)
subsetRowLinks(es, subsetName = "subset1")
#> LinkDataFrame with 5 rows and 5 columns
#>        nodeLab nodeLab_alias   nodeNum    isLeaf   whichTree
#>    <character>   <character> <integer> <logical> <character>
#> t2          t2       alias_1         1      TRUE       phylo
#> t7          t7       alias_2         2      TRUE       phylo
#> t6          t6       alias_3         3      TRUE       phylo
#> t9          t9       alias_4         4      TRUE       phylo
#> t4          t4       alias_5         5      TRUE       phylo