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Save a network to a file

save_network.Rd

Saves the whole network, including provenance (when and from which backend it was retrieved) and regulators, to an .rds file that load_network() reads back. Backends such as INDRA have no data versions, so the same query can give a different network later: save the network to keep the one an analysis used.

Usage

save_network(network, file)

Arguments

network

list of nodes and edges, e.g. from get_network() or merge_networks()

file

path of the file to write, ending in .rds

Value

file, invisibly

Details

The network is checked with validate_network() first. A network without provenance is saved with a warning: it is lost when a network is rebuilt with list(nodes = , edges = ).

See also

load_network()

Examples

network <- list(
    nodes = data.frame(
        id = c("CHK1_HUMAN", "CDC25A_HUMAN"),
        entity_type = "protein",
        entity_name = c("CHEK1", "CDC25A"),
        namespace = "HGNC",
        entity_id = c("1925", "1725"),
        measured = TRUE,
        included_in_query = TRUE,
        node_role = "passed_cutoffs"
    ),
    edges = data.frame(
        source = "CHK1_HUMAN",
        target = "CDC25A_HUMAN",
        interaction = "Phosphorylation",
        directed = TRUE,
        site = "S76",
        confidence = 0.99,
        evidence_count = 12L,
        evidence_url = paste0("https://db.indra.bio/statements/",
                                "from_hash/-1234?format=html"),
        statement_id = "-1234",
        backend_database = "INDRA",
        query_type = "subnetwork"
    ),
    provenance = data.frame(
        backend_database = "INDRA",
        query_type = "subnetwork",
        retrieved_at = as.POSIXct("2026-10-09 12:00:00", tz = "UTC")
    )
)
file <- tempfile(fileext = ".rds")
save_network(network, file)
identical(load_network(file), network)
#> [1] TRUE