convert to TreeSummarizedExperiment class object.

Usage

convert2TreeSummarizedExperiment(object, ...)

as.TreeSummarizedExperiment(object, ...)

# S3 method for class 'microbiome_dataset'
convert2TreeSummarizedExperiment(object, assay_name = "counts", ...)

Arguments

object: microbiomedataset
...: other params
assay_name: assay name used in the output object.

Value

TreeSummarizedExperiment class object.

Examples

if (requireNamespace("TreeSummarizedExperiment", quietly = TRUE)) {
  data("global_patterns", package = "microbiomedataset")
  x0 <- prune_taxa(global_patterns, variable_id = global_patterns@variable_info$variable_id[1:80])
  x <- convert2TreeSummarizedExperiment(x0)
  class(x)
}
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> [1] "TreeSummarizedExperiment"
#> attr(,"package")
#> [1] "TreeSummarizedExperiment"