BIOMconstants: Constants related to BIOM format

In BIOM.utils: Utilities for the BIOM (Biological Observation Matrix) Format

Description

These constants enumerate components of BIOM format and their valid values (controlled vocabularies).

Usage

biom_format
biom_format_url
biom_fields
biom_table_types
biom_matrix_element_types
biom_matrix_types

Details

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.

References

BIOM format
JSON

See Also

biom

Examples

biom_format_url [biom_format]
biom_fields
biom_table_types
biom_matrix_element_types
biom_matrix_types

Example output

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"

BIOM.utils documentation built on May 1, 2019, 7:32 p.m.