leafSummarizedExperiment-constructor: Construct a leafSummarizedExperiment object
In markrobinsonuzh/treeAGG: Tree Aggregation

Description Usage Arguments Value Author(s) See Also Examples

leafSummarizedExperiment is the constructor of the leafSummarizedExperiment class.

1	leafSummarizedExperiment(tree, ...)

tree

A phylo object.

...

For SummarizedExperiment, S4 methods list and matrix, arguments identical to those of the SimpleList method.

For rowRanges, ignored.

A leafSummarizedExperiment object

Ruizhu HUANG

leafSummarizedExperiment-class treeSummarizedExperiment-class SummarizedExperiment-class

# tree
data("tinyTree")

# the count table
count <- matrix(rpois(100, 50), nrow = 10)
rownames(count) <- c(tinyTree$tip.label)
colnames(count) <- paste("C_", 1:10, sep = "_")

# the sample information
sampC <- data.frame(condition = rep(c("control", "trt"),
                                    each = 5),
                    gender = sample(x = 1:2, size = 10,
                                    replace = TRUE))
rownames(sampC) <- colnames(count)

# build a leafSummarizedExperiment object
lse <- leafSummarizedExperiment(tree = tinyTree,
                                assays = list(count),
                                colData = sampC)