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Get the curations of edges from a backend

get_curations.Rd

Curators mark single pieces of evidence for a statement as correct or incorrect. get_curations() counts, for each statement, the evidence curated as incorrect. INDRA curations come from the INDRA database, with one request per statement. Most users call filter_by_curation(), which subtracts these counts from evidence_count.

Usage

get_curations(backend, edges, ...)

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

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

Arguments

backend

a NetworkBackend, e.g. from indra_backend()

edges

the edges of a network from get_network(). Needs the column statement_id.

...

passed to methods

Value

data.frame with one row per unique statement_id and the columns statement_id (character) and incorrect_count (integer). A failed request warns and counts as 0. A method for another backend may leave out statements with no curations, which filter_by_curation() counts as 0, but must return statement_id as character: filter_by_curation() errors otherwise, since a numeric hash can lose precision and match no edge.

See also

filter_by_curation()

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?
get_curations(indra, head(network$edges, 2))
#>         statement_id incorrect_count
#> 1  -5813063534036006               0
#> 2 -19747883270157675               0
# }