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Copy the values of an entity table onto a network's nodes

add_entity_values.Rd

Sets logFC and adj.pvalue of the nodes that match a row of entities, without querying a backend. Use it to show the results of another experiment on a network: for example, a network built from MSstatsPTM's ADJUSTED.Model, with its protein nodes colored by the global profiling results (PROTEIN.Model).

Usage

add_entity_values(network, entities, overwrite = FALSE)

Arguments

network

list of nodes and edges from get_network()

entities

entity table from prepare_entities(), grounded by convert_ids(). Its included_in_query column is ignored.

overwrite

whether to replace the logFC and adj.pvalue of node rows that already have them. FALSE (default) stops and names those nodes.

Value

network, with the values of entities on the matching nodes

Details

A node row matches an entity row with the same node id and site (for a PTM site row, its parent protein and site; for a protein, site = NA). Node rows that match no entity row by id are then matched by grounding (namespace and entity_id) and site. This finds nodes whose id is the backend's name, such as a kinase added with get_network(include_entities =) that INDRA calls "SRC", while the entity table has "P12931". An entity row that matched a node by id is not used again by grounding, so an isoform node doesn't take the values of its canonical protein. A node row that matches several entity rows gets no values, with a message.

A protein that has only PTM site rows in the network, and matches a protein-level entity row, gets a new protein-level row (site = NA) with that row's values, so cytoscapeNetwork() colors the protein node by it.

Matched node rows get measured = TRUE. Rows of entities that match no node are not added: get_network() decides which nodes are in the network. Edges and the other elements of network are unchanged. The node table does not record which experiment the values come from.

See also

filter_by_ptm_site(), merge_networks()

Examples

# A PTM network: phosphorylation of two EGFR sites by SRC, which is not
# in the PTM results, so it has INDRA's name as its id
network <- list(
    nodes = data.frame(
        id = c("P00533", "P00533", "SRC"),
        entity_type = c("ptm_site", "ptm_site", "protein"),
        entity_name = c("EGFR", "EGFR", "SRC"),
        namespace = "HGNC", entity_id = c("3236", "3236", "11283"),
        measured = c(TRUE, TRUE, FALSE), included_in_query = TRUE,
        node_role = c("passed_cutoffs", "passed_cutoffs", "user_added"),
        site = c("S1039", "Y1092", NA),
        has_measured_sites = c(TRUE, TRUE, FALSE),
        logFC = c(1.5, -0.4, NA), adj.pvalue = c(0.01, 0.3, NA)),
    edges = data.frame(
        source = "SRC", target = "P00533", interaction = "Phosphorylation",
        directed = TRUE, site = "Y1092", confidence = 0.9,
        evidence_count = 3L, evidence_url = "https://example.org/1",
        statement_id = "1", backend_database = "INDRA",
        query_type = "subnetwork")
)
# Global profiling results, grounded (convert_ids() would fill these)
global <- prepare_entities(
    data.frame(Protein = c("P00533", "P12931"), log2FC = c(0.2, 1.1),
               adj.pvalue = c(0.6, 0.02)),
    entity_type = "protein", id_type = "uniprot")
global$namespace <- "HGNC"
global$entity_id <- c("3236", "11283")
global$entity_name <- c("EGFR", "SRC")
network <- add_entity_values(network, global)
#> Copied the values of entities to 1 node row(s), and added a protein-level row to 1 protein(s) with only PTM site rows.
network$nodes[, c("id", "site", "measured", "logFC")]
#>       id  site measured logFC
#> 1 P00533  <NA>     TRUE   0.2
#> 2 P00533 S1039     TRUE   1.5
#> 3 P00533 Y1092     TRUE  -0.4
#> 4    SRC  <NA>     TRUE   1.1