getPPIbyEntrez: Extract the PPIs for my list of genes defined by Entrez IDs

In lptolik/synaptome.db: Synamptosome Proteome Database

Extract the PPIs for my list of genes defined by Entrez IDs

Description

Get Protein-Protein interactions (PPIs) for the set of ID. Function lookups for PPIs for the list of Entrez IDs and returns either “induced” (all available interactions for these genes) or “limited” (only interactions between genes specified in the query) table of interacting genes A and B, where A and B are respective Internal IDs.

Usage

getPPIbyEntrez(entrez, type = c("induced", "limited"))

Arguments

entrez	Entrez 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 getPPIbyIDs() 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(), getPPIbyIDs4BrainRegion(), getPPIbyIDs4Compartment(), getPPIbyIDs(), getPPIbyName(), getTableFromPPI()

Examples

t <- getPPIbyEntrez(c(1739, 1740, 1742, 1741), type = "ind")

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