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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_animalcules -

animalcules

convert_to_biomformat -

biomformat

convert_to_phyloseq -

phyloseq

convert_to_SE -

SummarizedExperiment

convert_to_TSE -

TreeSummarizedExperiment

Usage

convert_to_animalcules(biom, ...)

convert_to_biomformat(biom, ...)

convert_to_phyloseq(biom, ...)

convert_to_SE(biom, ...)

convert_to_TSE(biom, ...)

Arguments

biom

An rbiom object, or any value accepted by as_rbiom().

...

Not Used.

Value

An animalcules (MultiAssayExperiment), biomformat (biom), phyloseq, SummarizedExperiment, or TreeSummarizedExperiment object.

Details

animalcules, SummarizedExperiment, and biomformat objects include counts, metadata, and taxonomy.

phyloseq and TreeSummarizedExperiment additionally include the tree and sequences.

Examples

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

    print(hmp50)

    # Requires 'animalcules', a Bioconductor R package
    if (nzchar(system.file(package = "animalcules"))) {
      ani <- convert_to_animalcules(hmp50)
      print(ani)
    }

    # Requires 'biomformat', a Bioconductor R package
    if (nzchar(system.file(package = "biomformat"))) {
      bio <- convert_to_biomformat(hmp50)
      print(bio)
    }

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

    # 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)
    }
} # }