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Coerce a SummarizedExperiment object to a phyloseq object

Source: R/as_phyloseq.R
as_phyloseq.Rd

The phyloseq-package provides a suite of methods for working with 16S rRNA sequencing and other microbiome data that may be of use to the users of HMP16SData. The as_phyloseq method provides a means to easily coerce a SummarizedExperiment-class object to a phyloseq-class object.

Usage

as_phyloseq(x)

Arguments

x

A SummarizedExperiment-class object from the HMP16SData package

Value

A phyloseq-class object

Examples

V13() %>%
    as_phyloseq()
#> see ?HMP16SData and browseVignettes('HMP16SData') for documentation
#> loading from cache
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 33127 taxa and 2898 samples ]
#> sample_data() Sample Data:       [ 2898 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 33127 taxa by 6 taxonomic ranks ]
#> phy_tree()    Phylogenetic Tree: [ 33127 tips and 29546 internal nodes ]