getIGraphFromPPI: Get Igraph representation of PPI

In lptolik/synaptome.db: Synamptosome Proteome Database

Get Igraph representation of PPI

Description

Combine information from PPI data.frame obtained with functions like getPPIbyName or getPPIbyEntrez with information about genes obtained from getGenesByID to make interpretable undirected PPI graph in igraph format. In this format network could be further analysed and visualized by algorithms in igraph package.

Usage

getIGraphFromPPI(ppi)

Arguments

ppi	PPI data.frame with columns A and B, obtaioed from functions like getPPIbyName

Value

igraph object with specified PPI network.

See Also

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

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

Examples

library(igraph)
g <- getIGraphFromPPI(
    getPPIbyIDs(c(48, 129, 975, 4422, 5715, 5835), type = "lim")
)
plot(g, vertex.label = V(g)$RatName, vertex.size = 35)

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