\name{BAFSet}
\alias{BAFSet}
\title{Create a BAFSet object...}
\usage{BAFSet(locData, lrr, baf, pData, annotation="", universe, ...)
}
\description{Create a BAFSet object}
\details{This function is the preferred method for creating a new BAFSet object. Users are
generally discouraged from calling "new" directly. This BAFSet function enforces
the requirement for "lrr" and "baf" matrices.  These and any other "..." arguments will
become part of the assayData slot of the resulting object. "..." can be matrices or
DataFrame objects (from the IRanges package). This function passes
control to the "initGenoSet" method which performs argument checking including
dimname matching among relevant slots and sets everything to genome order. Genome
order can be disrupted by "[" or "[[" calls and will be checked by methods that
require it.}
\value{A BAFSet object}
\author{Peter M. Haverty}
\seealso{bafset-class, genoset-class}
\arguments{\item{locData}{A RangedData object specifying feature chromosome
locations. Rownames are required to match featureNames.}
\item{lrr}{numeric matrix of copy number data with rownames
matching sampleNames and colnames matching sampleNames}
\item{baf}{numeric matrix of B-Allele Frequency data with rownames
matching sampleNames and colnames matching sampleNames}
\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{...}{More matrix or DataFrame objects to include in assayData slot}
}
\examples{test.sample.names = LETTERS[11:13]
probe.names = letters[1:10]
locData.rd = RangedData(ranges=IRanges(start=c(1,4,3,2,5:10),width=1,names=probe.names),space=c(rep("chr1",4),rep("chr3",2),rep("chrX",4)),universe="hg18")
bs = BAFSet(
locData=locData.rd,
lrr=matrix(1:30,nrow=10,ncol=3,dimnames=list(probe.names,test.sample.names)),
baf=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"
)}