Accessor method for colLinks from subsets in ExperimentSubset objects

Get colLinks from a subset: the links of its columns to the nodes of the tree that subsetColTree returns.

Usage

subsetColLinks(x, subsetName, parentColLinkData = TRUE)

# S4 method for class 'SubsetTreeSummarizedExperiment'
subsetColLinks(x, subsetName, parentColLinkData = TRUE)

Arguments

x

ExperimentSubset Input ExperimentSubset object.

subsetName

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

parentColLinkData

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

Value

The colLinks of the subset's columns, with the subset's column names, 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)
subsetColLinks(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