xHubEnrich.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/networkAnalysis.R
\name{xHubEnrich}
\alias{xHubEnrich}
\title{Functional enrichment of x-hub neighborhood.}
\usage{
xHubEnrich(ig, go2eg)
}
\arguments{
\item{ig}{An igraph network object output from either 
\code{\link{adj2igraph}, \link{rankHub}, \link{cisTrans}}}

\item{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.}
}
\value{
Data.frame with each x-hub, out-degree, and the 
neighborhood percentage.
}
\description{
A means to assess functional 
impact of x-hub perturbations
}
\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
}
\seealso{
\code{\link{rankHub}}, \code{\link{cisTrans}}, 
\code{\link{reportHubs}}, \code{\link{adj2igraph}}
}