xHubEnrich: Functional enrichment of x-hub neighborhood.

In topherconley/spacemap: A novel conditional graphical model for integrative genomics

Description

A means to assess functional impact of x-hub perturbations

Usage

xHubEnrich(ig, go2eg)

Arguments

ig	An igraph network object output from either adj2igraph, rankHub, cisTrans
go2eg	Named list where the names denote a biological process (e.g. Gene Ontology ID) and the elements of the list is a vector of members belonging to the biological process. The list ought to be non-redundant in names.

Details

A x-hub is defined to be any x node with at least one edge to a y node. A x neighborhood comprises all y nodes that are directly connected to a x-hub by an edge. x neighborhoods are of interest because they represent direct perturbations to y nodes. To quantitatively assess how much those perturbations are functionally meaningful, we compute a score called the GO-neighbor percentage. Two y nodes are called GO-neighbors if they share a common Gene Ontology (GO) term in the same x neighborhood. We postulate that a high percentage of GO-neighbors within an x neighborhood associates the x-hub with more functional meaning. These scores, as presented in figure 5 of the spaceMap publication, can be generated with a GO mapping

Value

Data.frame with each x-hub, out-degree, and the neighborhood percentage.

See Also

rankHub, cisTrans, reportHubs, adj2igraph

topherconley/spacemap documentation built on May 31, 2019, 6:36 p.m.