importBIOM: Loading a BIOM file

In FelixErnst/mia: Microbiome analysis

Loading a BIOM file

Description

Loading a BIOM file

Usage

importBIOM(file, ...)

Arguments

file	BIOM file location
...	additional arguments to be passed to convertFromBIOM

Details

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

Value

importBIOM returns an object of class TreeSummarizedExperiment

See Also

importMetaPhlAn convertFromPhyloseq convertFromBIOM convertFromDADA2 importQIIME2 importMothur importHUMAnN

Examples

# 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)
                    

FelixErnst/mia documentation built on July 15, 2024, 9:21 p.m.