biomformat (version 1.0.2)

read_biom: Read a biom-format file, returning a biom-class.

Description

Import the data from a biom-format file into R, represented as an instance of the biom-class; essentially a list with special constraints that map to the biom-format definition.

Usage

read_biom(biom_file)

Arguments

biom_file

(Required). A character string indicating the file location of the biom formatted file. This is a HDF5 or JSON formatted file specific to biological datasets. The format is formally defined at the biom-format definition and depends on the versioning.

Value

An instance of the biom-class.

Details

The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project. Please see the biom-format home page for more details.

It is tempting to include an argument identifying the biom-format version number of the data file being imported. However, the biom-format version number is a required field in the biom-format definition. Rather than duplicate this formal specification and allow the possibility of a conflict, the version number of the biom format will be referred to only by the "format" field in the biom formatted data, or its representation in R.

References

http://biom-format.org/

See Also

Function to create a biom object from R data, make_biom.

Definition of the biom-class.

Function to write a biom format file from a biom object, write_biom

Accessor functions like header.

Examples

# # # import with default parameters, specify a file
biom_file <- system.file("extdata", "rich_sparse_otu_table.biom", package = "biomformat")
biom_file
read_biom(biom_file)
biom_file <- system.file("extdata", "min_sparse_otu_table.biom", package = "biomformat")
biom_file
read_biom(biom_file)
## The previous examples use system.file() because of constraints in specifying a fixed
##   path within a reproducible example in a package.
## In practice, however, you can simply provide "hard-link"
## character string path to your file:
# mybiomfile <- "path/to/my/biomfile.biom"
# read_biom(mybiomfile)