TreeSummarizedExperiment-accessor: TreeSummarizedExperiment-accessors

In fionarhuang/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, 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)

fionarhuang/TreeSummarizedExperiment documentation built on Aug. 18, 2021, 12:15 p.m.