This class inherits from the list-class
,
with validity checks specific to the definition to the
biom-format. Effectively this means the list must have
certain index names, some elements of which must have a
specific structure or value. For further details see
the
biom-format definition. Importantly, this means other
special properties of lists, like operations with
$
and single- or double-square-braces are also
supported; as-is the apply
-family function that
can operate on lists. Note that some features of the
biom-format can be essentially empty, represented by the
string "null"
in the file. These fields are
returned as NULL
when accessed by an
accessor function.
The constructor, biom
Accessor functions:
header
, biom_shape
,
nrow
, ncol
,
matrix_element_type
,
biom_data
,
observation_metadata
,
sample_metadata
1 2 3 4 5 6 7 8 9 10 11 12 | biom_file = system.file("extdata", "rich_sparse_otu_table.biom", package = "biom")
x = read_biom(biom_file)
header(x)
biom_shape(x)
nrow(x)
ncol(x)
rownames(x)
colnames(x)
matrix_element_type(x)
biom_data(x)
observation_metadata(x)
sample_metadata(x)
|
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