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Get the evidence behind network edges

get_evidence.Rd

Looks up the evidence sentences and their PubMed IDs for each edge, using the edge's statement_id. Edges that share a statement_id get the same evidence.

Usage

get_evidence(backend, edges, ...)

# S4 method for class 'NetworkBackend'
get_evidence(backend, edges, ...)

# S4 method for class 'IndraBackend'
get_evidence(backend, edges, ...)

Arguments

backend

a NetworkBackend, e.g. from indra_backend()

edges

the edges of a network from get_network(). Needs the columns source, target, interaction, site, evidence_url, and statement_id.

...

passed to methods

Value

data.frame with one row per (edge, evidence sentence) pair and the columns source, target, interaction, site, evidence_url, statement_id, text, and pmid. It has no rows, with a warning, when no edge has evidence text.

Details

For INDRA, the evidence comes from CoGEx. Evidence without text is left out, and pmid is "" for evidence from a source with no PubMed ID.

filterSubnetworkByContext() and the topic functions call get_evidence() with the backend named in each edge's backend_database, unless their backend argument is given.

See also

filterSubnetworkByContext()

Examples

# \donttest{
input <- data.table::fread(system.file(
    "extdata/groupComparisonModel.csv",
    package = "MSstatsBioNet"
))
indra <- indra_backend()
entities <- prepare_entities(input, entity_type = "protein",
                             id_type = "uniprot")
entities <- convert_ids(indra, entities)
entities <- select_entities(entities, pvalue_cutoff = 0.05)
network <- get_network(indra, entities, interaction_types = "Complex")
#> INDRA subnetwork: how are 10 selected proteins connected to each other, with no other nodes added?
evidence <- get_evidence(indra, head(network$edges, 2))
#> Processing 2 unique statement hashes...
#> Fetching evidence for 2 hashes in 1 batch(es) of up to 100...
#> Progress: 1/1 batches (100.0%)
#> Done fetching evidence!
#> Warning: No evidence text found for any statement hash
head(evidence[, c("source", "target", "pmid", "text")])
#> [1] source target pmid   text  
#> <0 rows> (or 0-length row.names)
# }