Analyses
Functional Profile Results
Return functional profile results as JSON. The returned JSON has the following top-level structure:
The
| Property | Description |
|---|---|
| n_mapped integer | The number of reads that were successfully mapped to a gene family or pathway. |
| n_reads integer | The number of reads present in the sample. |
| table array | An array of objects consisting of individual functional groups (format below). |
table array contains results across all functional groups and gene families, as well as taxonomic
information.
Each object in the array has the following fields:
| Property | Description |
|---|---|
| group_name string | The name of the functional group this result corresponds to. This will be one of the following: pathways, metacyc, eggnog, go, ko, ec, pfam, or reaction. |
| id string | A group-specific unique ID, e.g., GO:0006096, PF16874, COG0148. |
| metric string | The quantitative metric represented by the value field. This field will be one of the following values: cpm (counts per million), rpk (reads per kilobase), abundance, complete_abundance, or coverage. The abundance, complete_abundance and coverage metrics will only be present for pathway results, while cpm and rpk metrics are present for all other functional groups. |
| name string | The name of the function. |
| taxa_stratified boolean | A boolean indicating whether or not this result is associated with a specific organism. |
| taxon_id string | The NCBI taxonomy ID for the organism associated with this function. |
| taxon_name string | The name of the organism. |
| value number | Gene family or pathway abundance in the unit specified by the metric field. |
Warning: The above JSON format is specific to the current version of the functional analysis job. This format is stable and guaranteed to remain stable for this version of the job. However, future versions of the functional analysis job may alter the format or introduce new changes. Please use caution and include fallbacks when writing non-exploratory code using the above route. Please also feel free to reach out if you’d like to discuss this format and any forthcoming changes with us.