Skip to contents

Convert biom data to an external package class

Source: R/convert.r
convert_to.Rd

Converts your rbiom object into other common Bioconductor data structures. Each function requires the corresponding target package to be installed.

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 class), biomformat (biom class), phyloseq, SummarizedExperiment, or TreeSummarizedExperiment object.

Details

  • convert_to_animalcules(): Converts to a MultiAssayExperiment object tailored for the animalcules interactive microbiome analysis toolkit. Includes: counts, metadata, and taxonomy.

  • convert_to_biomformat(): Converts to a biom object used by the biomformat package, the standard Bioconductor class for reading and writing BIOM data. Includes: counts, metadata, and taxonomy.

  • convert_to_phyloseq(): Converts to a phyloseq object for use with the comprehensive phyloseq ecosystem. Includes: counts, metadata, taxonomy, phylogenetic tree, and sequences.

  • convert_to_SE(): Converts to a SummarizedExperiment object, a core SummarizedExperiment Bioconductor container for matrix-like data and annotations. Includes: counts, metadata, and taxonomy.

  • convert_to_TSE(): Converts to a TreeSummarizedExperiment object. This extends the SE class to natively support hierarchical TreeSummarizedExperiment relationships. Includes: counts, metadata, taxonomy, phylogenetic 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)
    }
} # }