\name{runSPIA}
\alias{runSPIA}
\title{Run SPIA analysis}
\description{
  Run topological analysis on expression dataset.
}
\usage{
runSPIA(de, all, pathwaySetName, ...)
}
\arguments{
  \item{de}{
    A named vector containing log2 fold-changes of the differentially
    expressed genes. The names of this numeric vector are Entrez gene IDs.
}
\item{all}{
  A vector with the Entrez IDs in the reference set. If the data was
  obtained from a microarray experiment, this set will contain all genes
  present on the specific array used for the experiment. This vector should contain all names of the 'de' argument.

}
\item{pathwaySetName}{
  A list of pathways like \link{kegg}, \link{nci} or \link{reactome}.
}
\item{\dots}{
  Additional options to pass to \code{\link[SPIA:spia]{spia}}.
}
}
\details{
The spia option "organism" is internally used. It is an error use it in
the additional options.
}
\value{
  The same of spia, without KEGG links. A data frame containing the ranked pathways and various statistics: pSize is the number of genes
on the pathway; NDE is the number of DE genes per pathway; tA is the observed total preturbation accumulation in the pathway; pNDE is the
probability to observe at least NDE genes on the pathway using a hypergeometric model; pPERT is the probability to observe a total
accumulation more extreme than tA only by chance; pG is the p-value obtained by combining pNDE and pPERT; pGFdr and pGFWER are the False
Discovery Rate and respectively Bonferroni adjusted global p-values; and the Status gives the direction in which the pathway is perturbed (activated or inhibited).
}
\references{
Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ,
Kusanovic JP, Romero R. A novel signaling pathway impact
analysis. Bioinformatics. 2009 Jan 1;25(1):75-82.

Adi L. Tarca, Sorin Draghici, Purvesh Khatri, et. al, A Signaling Pathway Impact Analysis for
Microarray Experiments, 2008, Bioinformatics, 2009, 25(1):75-82.

Draghici, S., Khatri, P., Tarca, A.L., Amin, K., Done, A., Voichita, C., Georgescu, C., Romero, R.:
A systems biology approach for pathway level analysis. Genome Research, 17, 2007.
}
\examples{
if (require(SPIA) && require(hgu133plus2.db)) {
  data(colorectalcancer)

  x <- hgu133plus2ENTREZID
  top$ENTREZ <- unlist(as.list(x[top$ID]))
  top <- top[!is.na(top$ENTREZ), ]
  top <- top[!duplicated(top$ENTREZ), ]
  tg1 <- top[top$adj.P.Val < 0.05, ]

  DE_Colorectal = tg1$logFC
  names(DE_Colorectal) <- as.vector(tg1$ENTREZ)
  ALL_Colorectal <- top$ENTREZ

  prepareSPIA(biocarta[1:20], "biocartaEx")
  runSPIA(de=DE_Colorectal, all=ALL_Colorectal, "biocartaEx")
}
}
\seealso{
  For other details please referer to \code{\link[SPIA:spia]{spia}}
}
\keyword{ spia }
\keyword{ analysis }
\keyword{ topology }