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, whichTree = 1, value)

## S4 method for signature 'TreeSummarizedExperiment'
rowTree(x, whichTree = 1, value)

rowTree(x, whichTree = 1) <- value

## S4 replacement method for signature 'TreeSummarizedExperiment'
rowTree(x, whichTree = 1) <- value

colTree(x, whichTree = 1)

## S4 method for signature 'TreeSummarizedExperiment'
colTree(x, whichTree = 1)

colTree(x, whichTree = 1) <- value

## S4 replacement method for signature 'TreeSummarizedExperiment'
colTree(x, whichTree = 1) <- value

rowTreeNames(x, value)

## S4 method for signature 'TreeSummarizedExperiment'
rowTreeNames(x, value)

rowTreeNames(x) <- value

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

colTreeNames(x, value)

## S4 method for signature 'TreeSummarizedExperiment'
colTreeNames(x, value)

colTreeNames(x) <- value

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

referenceSeq(x)

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

referenceSeq(x) <- value

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

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

## S4 replacement method for signature 
## 'TreeSummarizedExperiment,ANY,ANY,TreeSummarizedExperiment'
x[i, j, ...] <- value

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

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

subsetByLeaf(
  x,
  rowLeaf,
  colLeaf,
  whichRowTree,
  whichColTree,
  updateTree = TRUE
)

## S4 method for signature 'TreeSummarizedExperiment'
subsetByLeaf(
  x,
  rowLeaf,
  colLeaf,
  whichRowTree,
  whichColTree,
  updateTree = TRUE
)

subsetByNode(x, rowNode, colNode, whichRowTree, whichColTree)

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

Arguments

x

A TreeSummarizedExperiment object

whichTree

A numeric indicator or name character to specify which tree in the rowTree or colTree to be extracted. The default is to extract the first tree. If whichTree = NULL, a list of all trees is extracted.

value
  • the new rownames or colnames as a character value. See BiocGenerics.

  • A DNAStringSet object or an object coercible to one

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 []

rowLeaf

A vector of leaves that are used to subset rows. One could use the leaf number, or the leaf label to specify nodes, but not a mixture of them.

colLeaf

A vector of leaves that are used to subset columns. One could use the leaf number, or the leaf label to specify nodes, but not a mixture of them.

whichRowTree

A numeric indicator or name character to specify which tree in the rowTree.

whichColTree

A numeric indicator or name character to specify which tree in the colTree.

updateTree

TRUE or FALSE. Default is TRUE, which updates tree structures after subsetting.

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))

# the referenceSeq data
refSeq <- DNAStringSetList(one = DNAStringSet(rep("A",nrow(toy_tse))),
                           two = DNAStringSet(rep("B",nrow(toy_tse))))
referenceSeq(toy_tse) <- refSeq
toy_tse

# subset treeSE by leaves
library(ape)
set.seed(1)
z <- makeTSE(nrow = 5, ncol = 4, include.rowTree = TRUE, include.colTree = FALSE)
y <- makeTSE(nrow = 4, ncol = 4, include.rowTree = TRUE, include.colTree = FALSE)
tr <- ape::rtree(4)
zy <- rbind(z, y)
x <- changeTree(x = zy, rowTree = tr, whichRowTree = 2, rowNodeLab = tr$tip.label)
rowLinks(zy)
rowLinks(x)
## 1) rowLeaf exist only in one of trees
rf <- c("t1", "t3")
sx <- subsetByLeaf(x = x, rowLeaf = rf)
rowLinks(sx)

sx <- subsetByLeaf(x = x, rowLeaf = rf, updateTree = FALSE)
rowLinks(sx)

## 2) rowLeaf exist in all trees
rf <- 1:3
sxx <- subsetByLeaf(x = x, rowLeaf = rf)
rowLinks(sxx)



## 3) rowLeaf exist in all trees, but subset and update only the specified
trees
rf <- c(3:4)
sxx <- subsetByLeaf(x = x, rowLeaf = rf, whichRowTree = "phylo")
rowLinks(sxx)

[Package TreeSummarizedExperiment version 2.0.3 Index]