Convert a TreeSummarizedExperiment object to/from ‘BIOM’ results

For convenience, a few functions are available to convert BIOM, DADA2 and phyloseq objects to TreeSummarizedExperiment objects, and TreeSummarizedExperiment objects to phyloseq objects.

convertToBIOM(x, assay.type = "counts", ...)

importBIOM(file, ...)

convertFromBIOM(
  x,
  prefix.rm = removeTaxaPrefixes,
  removeTaxaPrefixes = FALSE,
  rank.from.prefix = rankFromPrefix,
  rankFromPrefix = FALSE,
  artifact.rm = remove.artifacts,
  remove.artifacts = FALSE,
  ...
)

# S4 method for class 'SummarizedExperiment'
convertToBIOM(x, assay.type = "counts", ...)

Arguments

x

TreeSummarizedExperiment

assay.type

Character scaler. The name of assay. (Default: "counts")

...

Additional arguments. Not used currently.

file

BIOM file location

prefix.rm

Logical scalar. Should taxonomic prefixes be removed? The prefixes is removed only from detected taxa columns meaning that rank.from.prefix should be enabled in the most cases. (Default: FALSE)

removeTaxaPrefixes

Deprecated. Use prefix.rm instead.

rank.from.prefix

Logical scalar. If file does not have taxonomic ranks on feature table, should they be scraped from prefixes? (Default: FALSE)

rankFromPrefix

Deprecated.Use rank.from.prefix instead.

artifact.rm

Logical scalar. If file have some taxonomic character naming artifacts, should they be removed. (default (Default: FALSE)

remove.artifacts

Deprecated. Use artifact.rm instead.

Value

convertFromBIOM returns an object of class TreeSummarizedExperiment

importBIOM returns an object of class TreeSummarizedExperiment

Details

convertFromBIOM coerces a biom object to a TreeSummarizedExperiment object.

convertToBIOM coerces a TreeSummarizedExperiment object to a biom object.

importBIOM loads a BIOM file and creates a TreeSummarizedExperiment object from the BIOM object contained in the loaded file.

See also

importQIIME2 importMothur

importMetaPhlAn convertFromPhyloseq convertFromBIOM convertFromDADA2 importQIIME2 importMothur importHUMAnN

Examples

# Convert BIOM results to a TreeSE
# Load biom file
library(biomformat)
biom_file <- system.file("extdata", "rich_dense_otu_table.biom",
                         package = "biomformat")

# Make TreeSE from BIOM object
biom_object <- biomformat::read_biom(biom_file)
tse <- convertFromBIOM(biom_object)

# Convert TreeSE object to BIOM
biom <- convertToBIOM(tse)

# Load biom file
library(biomformat)
biom_file <- system.file(
    "extdata", "rich_dense_otu_table.biom", package = "biomformat")

# Make TreeSE from biom file
tse <- importBIOM(biom_file)

# Get taxonomyRanks from prefixes and remove prefixes
tse <- importBIOM(
    biom_file, rank.from.prefix = TRUE, prefix.rm = TRUE)

# Load another biom file
biom_file <- system.file(
   "extdata", "Aggregated_humanization2.biom", package = "mia")

# Clean artifacts from taxonomic data
tse <- importBIOM(biom_file, artifact.rm = TRUE)