getPPIbyName: Extract the PPIs for my list of genes defined by Gene name

In lptolik/synaptome.db: Synamptosome Proteome Database

Extract the PPIs for my list of genes defined by Gene name

Description

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

Usage

getPPIbyName(name, type = c("induced", "limited"))

Arguments

name	Gene names
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

getPPIbyEntrez() 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(), getPPIbyEntrez(), getPPIbyIDs4BrainRegion(), getPPIbyIDs4Compartment(), getPPIbyIDs(), getTableFromPPI()

Examples

t <- getPPIbyName(
    c("CASK", "DLG4", "GRIN2A", "GRIN2B", "GRIN1"),
    type = "lim"
)

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