selNode: Select branches

In markrobinsonuzh/treeAGG: Tree Aggregation

Description

selNode selects branches meeting the specified criteria in the number of leaves and the count proportion.

Usage

selNode(obj = NULL, tree = NULL, data = NULL, minTip = 0,
  maxTip = Inf, minPr = 0, maxPr = 1, skip = NULL, all = FALSE)

Arguments

obj	A leafSummarizedExperiment object.
tree	A phylo object
data	A count table from the real data or a list output from parEstimate.
minTip	the minimum number of leaves in the selected branch
maxTip	The maximum number of leaves in the selected branch
minPr	The minimum count proportion of the selected branch in a sample. A value between 0 and 1.
maxPr	The maximum count proportion of the selected branch in a sample. A value between 0 and 1.
skip	A character vector of node labels. These nodes are not the descendants or the ancestors of the selected branch.
all	TRUE or FALSE. Default is FALSE. If FALSE, the branch node of a branch, which meet the requirements and has the minimum count proportion, is returned; otherwise branch nodes of all branches meeting the requirements are returned.

Value

The node whose descendant branch has the lowest proportion

Author(s)

Ruizhu Huang

Examples

set.seed(1)
data("tinyTree")
toyTable <- matrix(rnbinom(40, size = 1, mu = 10), nrow = 10)
colnames(toyTable) <- paste(rep(LETTERS[1:2], each = 2),
rep(1:2, 2), sep = "_")
rownames(toyTable) <- tinyTree$tip.label


dat <- parEstimate(data = toyTable)
(out1 <- selNode(tree = tinyTree, data = dat, all = TRUE))
(out2 <- selNode(tree = tinyTree, data = dat, minTip = 4, maxTip = 9,
minPr = 0, maxPr = 0.8, all = TRUE))

## provide obj
lse1 <- leafSummarizedExperiment(tree = tinyTree,
                                assays = list(toyTable))
out <- selNode(obj = lse1, all = TRUE)

markrobinsonuzh/treeAGG documentation built on May 26, 2019, 9:32 a.m.