BIOM (Biological Observation Matrix) is a simple prescription
for storing an annotated table of data.
It may be described as a format, standard, or data structure.The JSON (JavaScript Object Notation) standard
for expressing general data objects as text
is employed to define BIOM.
Therefore the native form of BIOM data is structured text,
conforming to the JSON specification in general
and the BIOM specification in particular.
Familiarity with BIOM is assumed here.
The S3 class biom
and its methods facilitate analyses
by expressing BIOM data as objects in the R environment.
Each function above transforms an object that is
already of class biom
into a basic R type.
as.matrix()
returns the BIOM data table as a matrix
.
If the object is "dense"
, then dimnames()
of the result
are equal to the BIOM row and column id
s.
Otherwise, the three-column sparse representation matrix is returned,
with ids
given by attached attributes "rownames"
and "colnames"
.
However, using expand=TRUE
expands a sparse representation.
(Setting expand=FALSE
has no effect when the object is "dense"
.)
Also, see below for an example using class "sparseMatrix"
from the R package Matrix.
as.character()
returns BIOM properly speaking, that is,
data and annotations written in JSON text conforming to the BIOM specification.
That text is written to file
, if provided.
See below for an example of saving the data table, only, in CSV or TSV format.
Of course, it is possible to bring biom
objects
in and out of the session with save()
and load()
.
as.list()
returns a list
corresponding closely
element-by-element to BIOM. The differences are:
list element data
is a matrix
not list
;
elements rows
and columns
hold metadata
only,
and so do not include id
s; instead, additional elements
row.ids
and column.ids
are present;
and format_url
is missing.