Convert biom data to an external package class

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. Rank names, metadata field names, and metadata column types are preserved. Sequences are included only when every OTU has one (requires the Biostrings package). 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. The tree and sequences are included when present. Includes: counts, metadata, taxonomy, phylogenetic tree, and sequences.

Examples

    library(rbiom)

    print(hmp50)
#> 
#> ══ Human Microbiome Project - 50 Sample Demo ═══════════════
#> 
#> Oral, nasal, vaginal, and fecal samples from a diverse set
#> of healthy volunteers. Source: Human Microbiome Project
#> (<https://hmpdacc.org>).
#> 
#>      50 Samples: HMP01, HMP02, HMP03, ..., and HMP50 
#>     490 OTUs:    Unc01yki, Unc53100, LtbAci52, ... 
#>       7 Ranks:   .otu, Kingdom, Phylum, ..., and Genus 
#>       5 Fields:  .sample, Age, BMI, Body Site, and Sex 
#>         Tree:    <present>
#> 
#> ── 182 - 22k reads/sample ──────────────────── 2023-09-22 ──
#> 

    # \donttest{
    # Requires 'animalcules' dependencies, Bioconductor R packages
    if (requireNamespace("MultiAssayExperiment", quietly = TRUE) &&
        requireNamespace("SummarizedExperiment", quietly = TRUE)) {
      ani <- convert_to_animalcules(hmp50)
      print(ani)
    }
#> A MultiAssayExperiment object of 1 listed
#>  experiment with a user-defined name and respective class.
#>  Containing an ExperimentList class object of length 1:
#>  [1] MicrobeGenetics: SummarizedExperiment with 490 rows and 50 columns
#> Functionality:
#>  experiments() - obtain the ExperimentList instance
#>  colData() - the primary/phenotype DataFrame
#>  sampleMap() - the sample coordination DataFrame
#>  `$`, `[`, `[[` - extract colData columns, subset, or experiment
#>  *Format() - convert into a long or wide DataFrame
#>  assays() - convert ExperimentList to a SimpleList of matrices
#>  exportClass() - save data to flat files

    # Requires 'biomformat', a Bioconductor R package
    if (requireNamespace("biomformat", quietly = TRUE)) {
      bio <- convert_to_biomformat(hmp50)
      print(bio)
    }
#> biom object. 
#> type: OTU table 
#> matrix_type: dense 
#> 490 rows and 50 columns 

    # Requires 'phyloseq', a Bioconductor R package
    if (requireNamespace("phyloseq", quietly = TRUE)) {
      phy <- convert_to_phyloseq(hmp50)
      print(phy)
    }
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 490 taxa and 50 samples ]
#> sample_data() Sample Data:       [ 50 samples by 4 sample variables ]
#> tax_table()   Taxonomy Table:    [ 490 taxa by 6 taxonomic ranks ]
#> phy_tree()    Phylogenetic Tree: [ 490 tips and 489 internal nodes ]
#> refseq()      DNAStringSet:      [ 490 reference sequences ]

    # Requires 'SummarizedExperiment', a Bioconductor R package
    if (requireNamespace("SummarizedExperiment", quietly = TRUE)) {
      se <- convert_to_SE(hmp50)
      print(se)
    }
#> class: SummarizedExperiment 
#> dim: 490 50 
#> metadata(0):
#> assays(1): OTU table
#> rownames(490): Unc01yki Unc53100 ... UncOr431 UncTr598
#> rowData names(6): Kingdom Phylum ... Family Genus
#> colnames(50): HMP01 HMP02 ... HMP49 HMP50
#> colData names(4): Age BMI Body Site Sex

    # Requires 'TreeSummarizedExperiment', a Bioconductor R package
    if (requireNamespace("TreeSummarizedExperiment", quietly = TRUE)) {
      tse <- convert_to_TSE(hmp50)
      print(tse)
    }
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> class: TreeSummarizedExperiment 
#> dim: 490 50 
#> metadata(0):
#> assays(1): OTU table
#> rownames(490): Unc01yki Unc53100 ... UncOr431 UncTr598
#> rowData names(6): Kingdom Phylum ... Family Genus
#> colnames(50): HMP01 HMP02 ... HMP49 HMP50
#> colData names(4): Age BMI Body Site Sex
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> reducedDimNames(0):
#> mainExpName: NULL
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> altExpNames(0):
#> rowLinks: a LinkDataFrame (490 rows)
#> rowTree: 1 phylo tree(s) (490 leaves)
#> colLinks: NULL
#> colTree: NULL
#> referenceSeq: a DNAStringSet (490 sequences)
    # }