rbiom (version 3.1.0)

convert_to: Convert biom data to an external package class

Description

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, ...)

Value

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

Arguments

biom

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

...

Not Used.

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) {
    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)
    }
}