changeTree {TreeSummarizedExperiment} | R Documentation |
changeTree
changes a row or column tree in a
TreeSummarizedExperiment
object.
changeTree( x, rowTree = NULL, rowNodeLab = NULL, colTree = NULL, colNodeLab = NULL, whichRowTree = 1, whichColTree = 1 )
x |
A TreeSummarizedExperiment object |
rowTree |
A phylo object. A new row tree. |
rowNodeLab |
A character string. It provides the labels of nodes that the rows of assays tables corresponding to. If NULL (default), the row names of the assays tables are used. |
colTree |
A phylo object. A new column tree. |
colNodeLab |
A character string. It provides the labels of nodes that the columns of assays tables corresponding to. If NULL (default), the column names of the assays tables are used. |
whichRowTree |
Which row tree to be replaced? Default is 1 (the first
tree in the |
whichColTree |
Which column tree to be replaced? Default is 1 (the first
tree in the |
A TreeSummarizedExperiment object
Ruizhu Huang
library(ape) set.seed(1) treeR <- ape::rtree(10) # the count table count <- matrix(rpois(160, 50), nrow = 20) rownames(count) <- paste0("entity", 1:20) colnames(count) <- paste("sample", 1:8, sep = "_") # The sample information sampC <- data.frame(condition = rep(c("control", "trt"), each = 4), gender = sample(x = 1:2, size = 8, replace = TRUE)) rownames(sampC) <- colnames(count) # build a TreeSummarizedExperiment object tse <- TreeSummarizedExperiment(assays = list(count), colData = sampC, rowTree = treeR, rowNodeLab = rep(treeR$tip.label, each =2)) treeR2 <- drop.tip(phy = treeR, tip = c("t10", "t9", "t8")) # if rownames are not used in node labels of the tree, provide rowNodeLab use <- changeTree(x = tse, rowTree = treeR2, rowNodeLab = rep(treeR$tip.label, each =2)) use # if rownames are used in node labels of tree, rowNodeLab is not required. rownames(tse) <- rep(treeR$tip.label, each =2) cse <- changeTree(x = tse, rowTree = treeR2) cse