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Convert an rbiom object to a SummarizedExperiment object.

Source: R/convert.r
convert_to_SE.Rd

Requires the relevant Bioconductor R package to be installed:

convert_to_SE -

SummarizedExperiment

convert_to_TSE -

TreeSummarizedExperiment

Usage

convert_to_SE(biom, ...)

convert_to_TSE(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 SummarizedExperiment or TreeSummarizedExperiment object.

Details

A SummarizedExperiment object includes counts, metadata, and taxonomy.

TreeSummarizedExperiment additionally includes the 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 ──
#> 
      
    # Requires 'SummarizedExperiment' Bioconductor R package
    if (nzchar(system.file(package = "SummarizedExperiment"))) {
      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' Bioconductor R package
    if (nzchar(system.file(package = "TreeSummarizedExperiment"))) {
      tse <- convert_to_TSE(hmp50)
      print(tse)
    }
#> 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
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: a LinkDataFrame (490 rows)
#> rowTree: 1 phylo tree(s) (490 leaves)
#> colLinks: NULL
#> colTree: NULL
#> referenceSeq: a DNAStringSet (490 sequences)