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Add a backend's properties of each entity

get_entity_properties.Rd

Adds one column per property, e.g. is_kinase. A property is NA for rows whose entity_type it doesn't apply to, and for rows the backend has no answer for. backend_capabilities(backend)$entity_properties lists the properties a backend supports.

Usage

get_entity_properties(backend, entities, properties = NULL, ...)

# S4 method for class 'NetworkBackend'
get_entity_properties(backend, entities, properties = NULL, ...)

# S4 method for class 'IndraBackend'
get_entity_properties(backend, entities, properties = NULL, ...)

Arguments

backend

a NetworkBackend, e.g. from indra_backend()

entities

entity table, grounded by convert_ids()

properties

the properties to add. NULL adds every property the backend supports.

...

passed to methods

Value

entities with one column per property

Details

For INDRA, the properties are is_transcription_factor, is_kinase, and is_phosphatase, looked up by gene symbol. Only rows with a single HGNC grounding get values. A PTM site gets the properties of its parent protein.

Examples

df <- data.frame(Protein = c("P04637", "Q00610"))
indra <- indra_backend()
entities <- prepare_entities(df, entity_type = "protein",
                             id_type = "uniprot")
entities <- convert_ids(indra, entities)
get_entity_properties(indra, entities, properties = "is_kinase")
#>       id entity_type id_type namespace entity_id entity_name included_in_query
#> 1 P04637     protein uniprot      HGNC     11998        TP53              TRUE
#> 2 Q00610     protein uniprot      HGNC      2092        CLTC              TRUE
#>   site parent_id organism is_kinase
#> 1 <NA>      <NA>     9606     FALSE
#> 2 <NA>      <NA>     9606     FALSE