Coerce a phyloseq object to a TreeSummarizedExperiment

Source: R/makeTreeSummarizedExperimentFromPhyloseq.R

makeTreeSEFromPhyloseq converts phyloseq objects into TreeSummarizedExperiment objects.

makeTreeSEFromPhyloseq(obj)

makeTreeSummarizedExperimentFromPhyloseq(obj)

# S4 method for ANY
makeTreeSummarizedExperimentFromPhyloseq(obj)

Arguments

obj

a phyloseq object

Value

An object of class TreeSummarizedExperiment

Details

All data stored in a phyloseq object is transferred.

Examples

if (requireNamespace("phyloseq")) {
    data(GlobalPatterns, package="phyloseq")
    makeTreeSEFromPhyloseq(GlobalPatterns)
    data(enterotype, package="phyloseq")
    makeTreeSEFromPhyloseq(enterotype)
    data(esophagus, package="phyloseq")
    makeTreeSEFromPhyloseq(esophagus)
}
#> class: TreeSummarizedExperiment 
#> dim: 58 3 
#> metadata(0):
#> assays(1): counts
#> rownames(58): 59_8_22 59_5_13 ... 65_9_9 59_2_6
#> rowData names(0):
#> colnames(3): B C D
#> colData names(0):
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: a LinkDataFrame (58 rows)
#> rowTree: 1 phylo tree(s) (58 leaves)
#> colLinks: NULL
#> colTree: NULL