\name{gcCorrect}
\alias{gcCorrect}
\title{cgCorrect}
\usage{
  gcCorrect(ds, gc, retain.mean = TRUE)
}
\arguments{
  \item{ds}{numeric matrix of copynumber or log2ratio
  values, samples in columns}

  \item{gc}{numeric vector, GC percentage for each row of
  ds, must not have NAs}

  \item{retain.mean}{logical, center on zero or keep same
  mean?}
}
\value{
  numeric matrix, residuals of ds regressed on gc
}
\description{
  Correct copy number for GC content
}
\details{
  Copy number estimates from various platforms show
  "Genomic Waves" (Diskin et al., Nucleic Acids Research,
  2008) where copy number trends with local GC content.
  This function regresses copy number on GC percentage and
  removes the effect (returns residuals). GC content should
  be smoothed along the genome in wide windows >= 100kb.
}
\examples{
gc = runif(n=100, min=1, max=100)
  ds = rnorm(100) + (0.1 * gc)
  gcCorrect(ds, gc)
}
\author{
  Peter M. Haverty
}
\seealso{
  Other "gc content": \code{\link{loadGC}},
  \code{\link{loadGC}}, \code{\link{loadGC}}
}