rowLinks {TreeSummarizedExperiment} | R Documentation |
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.
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]
x |
A TreeSummarizedExperiment object |
i, j |
The row, column index to subset |
... |
The argument from the subset function |
drop |
A logical value, TRUE or FALSE. The argument from the subset
function |
Elements from TreeSummarizedExperiment
.
Ruizhu HUANG
TreeSummarizedExperiment
SingleCellExperiment
# 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))