\name{collapseExpData}
\alias{collapseExpData}

\title{
  Combine multiple data sets
}

\description{
  This function takes a dataset with data from multiple experiments, and
  combines the data across multiple experiments according to a
  user-specified function. 
}

\usage{
collapseExpData(expData, tablename = NULL,
  what = getColnames(expData, all = FALSE), groups = "COL",
  collapse = c("sum", "avg", "weighted.avg"), overwrite = FALSE,
  deleteOriginal = FALSE, verbose = getOption("verbose"))
}
\arguments{
  \item{expData}{
    An object of class \code{ExpData}.
  }
  \item{tablename}{
    Name of database table to write output data to.
  }
  \item{what}{
    Data columns to apply \code{collapse} function to.
  }
  \item{groups}{
    Vector of length \code{what} indicating how columns should be
    grouped when applying \code{collapse} function. 
  }
  \item{collapse}{
    Function to apply to grouped columns.
  }
  \item{overwrite}{
    Logical indicating whether database referred to in \code{tablename} argument should be overwritten.
  }
  \item{deleteOriginal}{
    Logical indicating whether original database in \code{ExpData} object should be deleted.
  }
  \item{verbose}{
    Logical indicating whether details should be printed.
  }
}

\details{
  This function can be thought of as similar to \code{tapply},
  operating over the entries in the data set, applying the function
  specified in the \code{collapse} argument, grouping the data as
  indicated in the \code{groups} argument.
}
\value{
  Returns an object of class \code{ExpData}.
}

\author{ James Bullard \email{bullard@berkeley.edu}, Kasper Daniel
  Hansen \email{khansen@jhsph.edu} }

\seealso{ See \code{Genominator} vignette for more information.  }
\examples{
ed <- ExpData(system.file(package = "Genominator", "sample.db"),
              tablename = "raw")
nd <- importToExpData(head(ed, -1), dbFilename = tempfile(),
                      tablename = "collapsed")
head(nd)
cd <- collapseExpData(nd, tablename = "bio", overwrite = TRUE,
                      groups = c("mut", "mut", "wt", "wt"))
                      
head(cd)
}
\keyword{manip}