biom (version 0.3.12)

biom: Build and return an instance of the biom-class.

Description

This is for instantiating a biom object within R (biom-class), and assumes relevant data is already available in R. This is different than reading a biom file into R. If you are instead interested in importing a biom file into R, you should use the read_biom function. This function is made available (exported) so that advanced-users/developers can easily represent analogous data in this structure if needed. However, most users are expected to instead rely on the read_biom function for data import, followed by accessor functions that extract R-friendly subsets of the data stored in the biom-format derived list.

Usage

biom(x)

Arguments

x

(REQUIRED). A named list conforming to conventions arising from the fromJSON function reading a biom-format file with default settings. See read_biom for more details about data import and biom-class for more details about accessor functions that extract R-friendly subsets of the data and metadata stored in x.

Value

An instance of the biom-class.

Details

biom() is a constructor method. This is the main method suggested for constructing an experiment-level (biom-class) object from its component data.

See Also

The read_biom import function.

Accessor functions like header.

Examples

#
# import with default parameters, specify a file
biom_file = system.file("extdata", "rich_sparse_otu_table.biom", package = "biom")
x = read_biom(biom_file)
show(x)
print(x)
header(x)
biom_data(x)
biom_shape(x)
nrow(x)
ncol(x)
observation_metadata(x)
sample_metadata(x)