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Convert biom data to an external package class.

Source: R/convert.r
convert_to.Rd

Requires the relevant Bioconductor R package to be installed:

convert_to_phyloseq -

phyloseq

convert_to_SE -

SummarizedExperiment

convert_to_TSE -

TreeSummarizedExperiment

Usage

convert_to_SE(biom, ...)

convert_to_TSE(biom, ...)

convert_to_phyloseq(biom, ...)

Arguments

biom

An rbiom object, such as from as_rbiom(). Any value accepted by as_rbiom() can also be given here.

...

Not Used.

Value

A phyloseq, SummarizedExperiment, or TreeSummarizedExperiment object.

Details

A SummarizedExperiment object includes counts, metadata, and taxonomy.

phyloseq and TreeSummarizedExperiment additionally includes the tree and sequences.

Examples

if (FALSE) { # \dontrun{
    library(rbiom)

    print(hmp50)

    # Requires 'phyloseq', a Bioconductor R package
    if (nzchar(system.file(package = "phyloseq"))) {
      physeq <- convert_to_phyloseq(hmp50)
      print(physeq)
    }

    # Requires 'SummarizedExperiment', a Bioconductor R package
    if (nzchar(system.file(package = "SummarizedExperiment"))) {
      se <- convert_to_SE(hmp50)
      print(se)
    }

    # Requires 'TreeSummarizedExperiment', a Bioconductor R package
    if (nzchar(system.file(package = "TreeSummarizedExperiment"))) {
      tse <- convert_to_TSE(hmp50)
      print(tse)
    }
} # }