\name{pePathway}
\alias{pePathway}
\alias{pePathway-class}
\title{Class that encodes the result of Pathway-Express for a single pathway}
\description{
  Class that encodes the result of Pathway-Express for a
  single pathway
}
\section{Slots}{
  \describe{ \item{\code{map}:}{an object of type graph
  (e.g., \code{\link{graphNEL}}).}
  \item{\code{input}:}{named vector of fold changes for
  genes on this pathway. The names of the genes are the
  orignal IDS used in the analysis}
  \item{\code{ref}:}{vector of reference IDs on this
  pathway} \item{\code{boot}:}{an object of class
  \code{boot} encoding the bootstrap information.}
  \item{\code{Pert}:}{the gene perturbation factors for all
  genes on the pathway, as computed by Pathway-Express.}
  \item{\code{Acc}:}{the gene accumulations for all genes
  on the pathway, as computed by Pathway-Express.} }
}
\author{
  Calin Voichita and Sorin Draghici
}
\seealso{
  \code{\link{pe}}, \code{\link{peRes}}
}