getPPIbyIDs: Extract the PPIs for my list of genes defined by GeneID

In lptolik/synaptome.db: Synamptosome Proteome Database

Extract the PPIs for my list of genes defined by GeneID

Description

Get Protein-Protein interactions (PPIs) for the set of internal GeneIDs. Function lookups for PPIs for specific GeneID and returns either “induced” (all interaction for this GeneID) or “limited” (only interactions between GeneIDs specified in the query) table of A and B interacting genes, where A and B are respective GeneIDs.

Usage

getPPIbyIDs(ids, type = c("induced", "limited"))

Arguments

ids	Gene IDs
type	type of the PPI network should be either induced (for all the PPIs for specific genes, including external genes) or limited (for PPIs between the genes specified in the query). Type could be shortened to recognizable minimum like 'ind' or 'lim'.

Value

data.frame with interactors internal GeneID in columns A and B

See Also

getPPIbyName() and getPPIbyEntrez() to get PPI data.frame, getIGraphFromPPI() to get igraph representation of the PPI data.frame and getTableFromPPI() to get interpretable table representation of the PPI data.frame.

Other PPI functions: getIGraphFromPPI(), getPPIbyEntrez(), getPPIbyIDs4BrainRegion(), getPPIbyIDs4Compartment(), getPPIbyName(), getTableFromPPI()

Examples

t <- getPPIbyIDs(c(48, 585, 710), type = "limited") # (16 rows)
t <- getPPIbyIDs(c(48, 585, 710), type = "induced") # 306 rows

lptolik/synaptome.db documentation built on Sept. 13, 2023, 2:50 p.m.