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\name{laplacianFromA}
\alias{laplacianFromA}

\title{Calculates the Laplacian associated to an adjacency matrix}

\description{
Calculates the Laplacian associated to an adjacency matrix.
}

\usage{laplacianFromA(A, k=1, ltype=c("meanInfluence", "normalized", "unnormalized", "totalInfluence"))}

\arguments{
\item{A}{The adjacency matrix of the graph.}
\item{k}{...}
\item{ltype}{A \code{\link[base]{character}} value specifying the type of Laplacian to be
calculated.  Defaults to meanInfluence.}
}

\value{
A \code{\link[base]{list}} containing the following components:
\describe{
\item{U}{Eigenvectors of the graph Laplacian.}
\item{l}{Eigenvalues of the graph Laplacian}
\item{kIdx}{Multiplicity of '0' as eigenvalue.}
}
}

\author{Laurent Jacob, Pierre Neuvial and Sandrine Dudoit}

\examples{
library("KEGGgraph")
library("rrcov")

## Create a random graph
graph <- randomWAMGraph(nnodes=5, nedges=7, verbose=TRUE)
plot(graph)

## write it to KGML file
grPathname <- "randomWAMGraph.xml"

gr <- parseKGML2Graph(grPathname)

## Two examples of Laplacians from the same graph
lapMI <- laplacianFromA(A, ltype="meanInfluence")
print(lapMI)

lapN <- laplacianFromA(A, ltype="normalized")
print(lapN)

U <- lapN$U p <- nrow(A) sigma <- diag(p)/sqrt(p) X <- twoSampleFromGraph(100, 120, shiftM2=1, sigma, U=U, k=3) ## T2 t <- T2.test(X$X1,X$X2) str(t) tu <- graph.T2.test(X$X1, X\$X2, lfA=lapMI, k=3)
str(tu)
}