Description Usage Arguments Details Value See Also Examples
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.
1 | 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
.
The read_biom
import function.
Accessor functions like header
.
1 2 3 4 5 6 7 8 9 10 11 12 13 | #
# 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)
|
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