mia: Microbiome analysis

importBIOM

R Documentation

Convert a `TreeSummarizedExperiment` object to/from ‘BIOM’ results

Description

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

Usage

importBIOM(file, ...)

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

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

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

Arguments

`file`	BIOM file location
`...`	Additional arguments. Not used currently.
`x`	`TreeSummarizedExperiment`
`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.
`assay.type`	`Character scaler`. The name of assay. (Default: `"counts"`)

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.

Value

convertFromBIOM returns an object of class TreeSummarizedExperiment

importBIOM returns an object of class TreeSummarizedExperiment

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)

microbiome/mia documentation built on Sept. 19, 2024, 11:17 p.m.