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Keep the edges that modify a PTM site in the network

filter_by_ptm_site.Rd

Keeps an edge when its site is one of the PTM sites of its target, that is, of a node row with the target's id. For a network built from MSstatsPTM results, these are the edges that explain a site in the input, e.g. a kinase phosphorylating a site whose phosphorylation changed. Each edge is checked on its own, so the order of this filter and filter_by_curation() doesn't matter.

Usage

filter_by_ptm_site(network)

Arguments

network

list of nodes and edges from get_network(), with PTM site rows in nodes (entity tables with entity_type = "ptm_site")

Value

network, with the edges whose site is not a site of their target removed, and the nodes they leave without edges. Stops when no edges remain.

Details

Edges without a site are dropped. These include every edge that isn't a modification (Complex, Activation, ...), and every edge from a backend that reports no sites, such as STRING: filter an INDRA network before merging it with one from such a backend, if those edges should stay. Nodes are dropped when they had edges and lost them all. Nodes that had no edge, and other elements of network, such as provenance, are kept.

Node sites are split on "_" (several sites of one peptide, e.g. "S1039_S1042") and ";" (members of a protein group); edge sites on ";".

See also

add_entity_values()

Examples

# A phosphorylation network of CPTAC CCRCC sites and ten kinases, saved
# by inst/script/cptac-ccrcc-network.R
saved <- readRDS(system.file("extdata/cptac-ccrcc-network.rds",
                             package = "MSstatsBioNet"))
network <- filter_by_ptm_site(saved$network)
#> Dropping 580 edge(s) whose site is not a PTM site of their target in the network.
head(network$edges[, c("source", "target", "site")])
#>     source                target site
#> 31   PRKCA  sp|P29353|SHC1_HUMAN S139
#> 144  MAPK1   sp|P29590|PML_HUMAN  S36
#> 147  MAPK1   sp|P29590|PML_HUMAN  S38
#> 148  MAPK1 sp|P78536|ADA17_HUMAN T735
#> 157  MAPK1   sp|P29590|PML_HUMAN  S40
#> 213  PRKCA sp|P78536|ADA17_HUMAN T735