Description Usage Details References See Also Examples
These constants enumerate components of BIOM format and their valid values (controlled vocabularies).
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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.
biom_format
gives the latest BIOM version implemented by this package.
biom_format_url
gives its associated URL.
biom_fields
lists the components specified by BIOM.
Each other constant enumerates the allowed values of its corresponding BIOM component.
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BIOM.utils (0.9 dbcb27)
Biological Observation Matrix 1.0
"http://biom-format.org/documentation/format_versions/biom-1.0.html"
[1] "rows" "columns" "data"
[4] "shape" "matrix_type" "matrix_element_type"
[7] "type" "format" "format_url"
[10] "date" "id" "generated_by"
[1] "OTU table" "Pathway table" "Function table" "Ortholog table"
[5] "Gene table" "Metabolite table" "Taxon table"
[1] "int" "float" "unicode"
[1] "dense" "sparse"
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