getPPIbyIDs4Compartment: Prepare induced or limited network for compartment

In lptolik/synaptome.db: Synamptosome Proteome Database

Prepare induced or limited network for compartment

Description

Prepare PPI network for genes from your list annotated for specific compartment. Should be used with findGenesByEntrez or findGenesByName functions to obtain list of internal IDs for your list of genes. Could be used with getAllGenes4Compartment functions to obtain all genes belonging to respective compartment. Function lookups the PPI table for gene IDs from the list and returns “limited” or “induced” interactors GeneIDs from the same compartment.

Usage

getPPIbyIDs4Compartment(ids, compartmentID, type = c("induced", "limited"))

Arguments

ids	internal gene IDs
compartmentID	ID for specific compartment
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

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

Other Compartment functions: getAllGenes4Compartment(), getCompartments(), getGenes4Compartment()

Examples

ppi <- getPPIbyIDs4Compartment(c(1, 15, 156, 1500, 3000, 7000),
    compartmentID = 1, type = "induced"
) # 201 rows

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