\name{initGenoSet}
\alias{initGenoSet}
\title{Create a GenoSet or derivative object}
\usage{
  initGenoSet(type, locData, pData = NULL, annotation = "",
    universe = NULL, assayData = NULL, ...)
}
\arguments{
  \item{type}{character, the type of object (e.g. GenoSet,
  BAFSet, CNSet) to be created}

  \item{locData}{A RangedData object specifying feature
  chromosome locations. Rownames are required to match
  featureNames.}

  \item{pData}{A data frame with rownames matching all data
  matrices}

  \item{annotation}{character, string to specify
  chip/platform type}

  \item{universe}{character, a string to specify the genome
  universe for locData}

  \item{assayData}{assayData, usually an environment}

  \item{...}{More matrix or DataFrame objects to include in
  assayData}
}
\value{
  A GenoSet object or derivative as specified by "type" arg
}
\description{
  This function is the preferred method for creating a new
  GenoSet object. Users are generally discouraged from
  calling "new" directly. The "..." argument is for any
  number of matrices of matching size that will become part
  of the assayData slot of the resulting object. This
  function passes control to the "genoSet" object which
  performs argument checking including dimname matching
  among relevant slots and sets everything to genome order.
  Genome order can be disrupted by "[" calls and will be
  checked by methods that require it.
}
\examples{
test.sample.names = LETTERS[11:13]
  probe.names = letters[1:10]
  gs = GenoSet(
     locData=RangedData(ranges=IRanges(start=1:10,width=1,names=probe.names),space=c(rep("chr1",4),rep("chr3",2),rep("chrX",4)),universe="hg18"),
     cn=matrix(31:60,nrow=10,ncol=3,dimnames=list(probe.names,test.sample.names)),
     pData=data.frame(matrix(LETTERS[1:15],nrow=3,ncol=5,dimnames=list(test.sample.names,letters[1:5]))),
     annotation="SNP6"
  )
}
\author{
  Peter M. Haverty
}