Build and return an instance of the biom-class.
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.
biom(x) ## S4 method for signature 'list' biom(x)
x |
(REQUIRED). A named list conforming to conventions arising from
the |
biom() is a constructor method. This is the main method
suggested for constructing an experiment-level (biom-class)
object from its component data.
An instance of the biom-class.
Function to create a biom object from R data,
make_biom.
Definition of the
biom-class.
The read_biom import function.
Function to write a biom format file from a biom object,
write_biom
Accessor functions like header.
#
# import with default parameters, specify a file
biom_file = system.file("extdata", "rich_sparse_otu_table.biom", package = "biomformat")
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.