Questions you can ask of a network backend
network_queries.RdEach query constructor asks one question of a backend. Pass the query to
get_network(). Every query returns the same nodes
and edges tables (see validate_network()), so
visualization and filtering work the same whichever question produced
the network. The query_type column of edges names the
query, without _query.
Details
| Constructor | Question | Nodes added | query_type |
subnetwork_query() | How are my selected entities connected to each other, with no other nodes added? | none, other
than include_entities | "subnetwork" |
More queries (shared regulators, regulator enrichment, paths, and
others) are planned. backend_capabilities(backend)$query_types lists the
ones a backend supports.
Glossary
- entity
One row of the entity table from
prepare_entities(): one analyte of the input, such as a protein, a PTM site, or a metabolite.- selected
An entity with
included_in_query = TRUE, set byselect_entities(): it passed the cutoffs, or was forced in. Only selected entities are sent to the backend.- in the input (
measured) A node that matches a row of the entity table, whether or not it was selected. It carries that row's statistics.
- latent
A node that matches no row of the entity table, such as an entity added through
include_entities. It hasmeasured = FALSEandNAstatistics. It may still have been measured in another experiment, or filtered out before the entity table was built.- grounding
A
"namespace:identifier"pair that names an entity in a backend, such as"HGNC:11998"(TP53).