\name{runCBS}
\alias{runCBS}
\title{Run CBS Segmentation}
\usage{runCBS(data, locs, return.segs=FALSE, n.cores=getOption("cores"), smooth.region=2, outlier.SD.scale=4, smooth.SD.scale=2, trim=0.025)
}
\description{Utility function to run CBS's three functions on one or more samples}
\details{Takes care of running CBS segmentation on one or more samples. Makes appropriate
input, smooths outliers, and segment}
\alias{runCBS}
\alias{segment}
\alias{segmentation}
\value{data frame of segments from CBS}
\author{Peter M. Haverty}
\arguments{\item{data}{numeric matrix with continuous data in one or more columns}
\item{locs}{RangeData, like locData slot of GenoSet}
\item{return.segs}{logical, if true list of segment data.frames return, otherwise a DataFrame of Rle vectors. One Rle per sample.}
\item{n.cores}{numeric, number of cores to ask multicore to use}
\item{smooth.region}{number of positions to left and right of individual positions to consider when smoothing single point outliers}
\item{outlier.SD.scale}{number of SD single points must exceed smooth.region to be considered an outlier}
\item{smooth.SD.scale}{floor used to reset single point outliers}
\item{trim}{fraction of sample to smooth}
}
\examples{sample.names = paste("a",1:2,sep="")
probe.names =  paste("p",1:30,sep="")
ds = matrix(c(c(rep(5,20),rep(3,10)),c(rep(2,10),rep(7,10),rep(9,10))),ncol=2,dimnames=list(probe.names,sample.names))
locs = RangedData(ranges=IRanges(start=c(1:20,1:10),width=1,names=probe.names),space=paste("chr",c(rep(1,20),rep(2,10)),sep=""))

seg.rle.result = DataFrame( a1 = Rle(c(rep(5,20),rep(3,10))), a2 = Rle(c(rep(2,10),rep(7,10),rep(9,10))), row.names=probe.names )
seg.list.result = list(
a1 = data.frame( ID=rep("a1",2), chrom=factor(c("chr1","chr2")), loc.start=c(1,1), loc.end=c(20,10), num.mark=c(20,10), seg.mean=c(5,3), stringsAsFactors=FALSE),
a2 = data.frame( ID=rep("a2",3), chrom=factor(c("chr1","chr1","chr2")), loc.start=c(1,11,1), loc.end=c(10,20,10), num.mark=c(10,10,10), seg.mean=c(2,7,9), stringsAsFactors=FALSE)
)

runCBS(ds,locs)  # Should give seg.rle.result
runCBS(ds,locs,return.segs=TRUE) # Should give seg.list.result}