\name{KEGGHyperGParams-class}
\docType{class}
\alias{KEGGHyperGParams-class}
\alias{PFAMHyperGParams-class}

\title{Class "KEGGHyperGParams" and "PFAMHyperGParams"}
\description{
  Parameter classes for representing all parameters needed for
  running the \code{hyperGTest} method with KEGG or PFAM as the
  category.
}

\section{Objects from the Class}{
Objects can be created by calls of the form
\code{new("KEGGHyperGParams", ...)} or 
\code{new("PFAMHyperGParams", ...)}.
}
\section{Slots}{
  \describe{
    \item{\code{geneIds}:}{Object of class \code{"ANY"}: A vector of
      gene identifiers.  Numeric and character vectors are probably the
      only things that make sense.  These are the gene ids for the
      selected gene set.}
    \item{\code{universeGeneIds}:}{Object of class \code{"ANY"}: A
      vector of gene ids in the same format as \code{geneIds} defining a
      subset of the gene ids on the chip that will be used as the
      universe for the hypergeometric calculation.  If this is
      \code{NULL} or has length zero, then all gene ids on the chip will
      be used.}
    \item{\code{annotation}:}{A string giving the name of the
      annotation data package for the chip used to generate the data.}
    \item{\code{cateogrySubsetIds}:}{Object of class \code{"ANY"}:
      If the test method supports it, can be used to specify a subset of
      category ids to include in the test instead of all possible
      category ids.}
    \item{\code{categoryName}:}{A string describing the category.
      This will be automatically set to "KEGG" or "PFAM" via the
      class's prototype.}

    \item{\code{pvalueCutoff}:}{The p-value to use as a cutoff for
        significance for testing methods that require it.  This value
        will also be passed on to the result instance and used for
        display and counting of significant results.  The default is 0.01.}

    \item{\code{testDirection}:}{A string indicating whether the
      test should be for overrepresentation (\code{"over"}) or
      underrepresentation (\code{"under"}).}

  }
}
\section{Extends}{
Class \code{"HyperGParams"}, directly.
}
\section{Methods}{
  \describe{
    \item{hyperGTest}{\code{signature(p =
        "HyperGParams")}: Perform hypergeometric tests to
      assess overrepresentation of category ids in the gene set.  See
      the documentation for the generic function for details.  This
      method must be called with a proper subclass of
      \code{HyperGParams}.}
  }
}

\author{S. Falcon}

\seealso{
  \code{\link{HyperGResult-class}}
  \code{\link{GOHyperGParams-class}}
  \code{\link{geneKeggHyperGeoTest}}
  \code{\link{hyperGTest}}
}

\keyword{classes}