\name{mergeBGMat}
\alias{mergeBGMat}

\title{A function that merges two bipartite graph (BG) incidence
  matrices into one.}
\description{
  This function takes the union of the row names of mat1 and mat2
  for the row names of the aggregate matrix, and takes the union of the
  complexes of mat1 and mat2. The resulting matrix is also an incidence
  matrix so an entry of unity impiles protein p is a member of complex C.
}
\usage{
mergeBGMat(mat1, mat2, toBeRm)
}

\arguments{
  \item{mat1}{The first bipartite graph incidence matrix}
  \item{mat2}{The second bipartite graph incidence matrix}
  \item{toBeRm}{A character vector of complexes to be removed}
}

\details{
  This function takes two bipartite graph matrices and merges them into
  one aggregate incidence matrix where informational redundancy is
  removed.

  The rows of the aggregate matrix is indexed by the union of the
  rownames of mat1 and mat2. It is important that the rownames of mat1
  and the rownames of mat2 are from the same name set (e.g. for yeast,
  only the standard gene names should be used).

  The columns will be indexed by different protein complexes. If two
  protein complexes are identical, say C-i = K-j, then either C-i or K-j
  should be listed in toBeRm argument (given as an argument). When the
  matrices are merged, only one of the two will be kept. The vector
  toBeRm is generated by calling either \code{\link{runCompareComplex}}
  or \code{\link{findSubComp}}.
}

\value{
  An aggregate bipartite graph incidence matrix.
}
\author{ Tony Chiang }

\examples{
#go = getGOInfo()
#mips = getMipsInfo()
#goM = createGOMatrix(go)
#mipsM = createMipsMatrix(mips)
#cc = runCompareComplex(mipsM, goM, byWhich = "ROW")
#merged = mergeBGMat(mipsM, goM, cc$toBeRm)
}
\keyword{datagen}
\keyword{array}