\name{Summary}
\alias{Summary}
\alias{Summary,peRes-method}
\alias{Summary.peRes}
\title{Summarize the results of a Pathway-Express analysis}
\arguments{
\item{x}{Pathways-Express result object obtained using

\item{pathNames}{named vector of pathway names; the names
of the vector are the IDs of the pathways}

\item{totalAcc}{boolean value indicating if the total
accumulation should be computed}

\item{totalPert}{boolean value indicating if the total
perturbation should be computed}

\item{normalize}{boolean value indicating if
normalization with regards to the boostrap simulations
should be performed on totalAcc and totalPert}

\item{pPert}{boolean value indicating if the significance
of the total perturbation in regards to the bootstrap
permutations should be computed}

\item{pAcc}{boolean value indicating if the significance
of the total accumulation in regards to the bootstrap
permutations should be computed}

\item{pORA}{boolean value indicating if the
over-represtation p-value should be computed}

\item{comb.pv}{vector of the p-value names to be combine
(any of the above p-values)}

\item{comb.pv.func}{the function to combine the p-values;
takes as input a vector of p-values and returns the
combined p-value}

\item{order.by}{the name of the p-value that is used to
order the results}

}
\description{
Summarize the results of a Pathway-Express analysis
}
\examples{
fc <- top$logFC[top$adj.P.Val <= .01]
names(fc) <- top$entrez[top$adj.P.Val <= .01]
ref <- top\$entrez

# load the set of pathways
kpg <- keggPathwayGraphs("hsa")
kpg <- setEdgeWeights(kpg)
kpg <- setNodeWeights(kpg, defaultWeight = 1)

# perform the pathway analysis
peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)

# obtain summary of results