@@ -11,6 +11,7 @@ export(calculatePowerDetectSomatic)

 export(calculateTangentNormal)

 export(callAlterations)

 export(callAlterationsFromSegmentation)

+export(callCIN)

 export(callLOH)

 export(callMutationBurden)

 export(correctCoverageBias)

new file mode 100644

@@ -0,0 +1,43 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/callCIN.R

+\name{callCIN}

+\alias{callCIN}

+\title{Call Chromosomal Instability}

+\usage{

+callCIN(res, id = 1, allele.specific = TRUE,

+  reference.state = c("dominant", "normal"))

+}

+\arguments{

+\item{res}{Return object of the \code{\link{runAbsoluteCN}} function.}

+

+\item{id}{Candidate solution to extract CIN from. \code{id=1} will use the

+maximum likelihood solution.}

+

+\item{allele.specific}{Use allele-specific or only total copy number for

+detecting abnormal regions. Copy-number neutral LOH would be ignored when

+this parameter is set to \code{FALSE}.}

+

+\item{reference.state}{Copy number regions different from the reference

+state are counted as abnormal. Default is \code{dominant} means the most

+common state. The other option is \code{normal}, which defines normal

+heterozygous, diploid as reference. The default is robust to errors in

+ploidy.}

+}

+\value{

+Returns \code{double(1)} with CIN value.

+}

+\description{

+This function provides detailed CIN information.

+}

+\examples{

+

+data(purecn.example.output)

+head(callCIN(purecn.example.output))

+

+}

+\seealso{

+\code{\link{runAbsoluteCN}}

+}

+\author{

+Markus Riester

+}