R/doPSCN.R

In jointseg: Joint segmentation of multivariate (copy number) signals

doPSCN <- structure(function(#Run PSCN segmentation (defunct)
### The 'PSCN' package is not maintained anymore and it is not available for
### R >= 3.0.0.  The original 'doPSCN' function has been moved to the directory
### 'zzz.defunct'.  The skeleton of that function is kept for backward
### compatibility.
                             Y,
### The signal to be segmented, a matrix containing the following columns: \describe{
### \item{c}{Total copy number (log scale)}
### \item{b}{Allele B fraction (a.k.a. BAF)}
### }
                             alpha=0.01,
### sensitivity level in [0,1] to be passed to
### \code{PSCN::segmentation}.
                             platform=c("Illumina", "Affymetrix"),
### Specifies form which array platform 'Y' was generated: Illumina or Affymetrix
                             verbose=FALSE,
### A \code{logical} value: should extra information be output ? Defaults to \code{FALSE}.
                             ...
### Further arguments to be passed to \code{PSCN::smoothing}
                             ) {
    ##references<<Chen, H., Xing, H., & Zhang, N. R. (2011). Estimation
    ##of parent specific DNA copy number in tumors using high-density
    ##genotyping arrays. PLoS computational biology, 7(1), e1001060.

    ##seealso<<\code{\link{PSSeg}}
    stop("The 'PSCN' package is not available for R >= 3.0.0.\nSee http://cran.r-project.org/web/packages/PSCN/index.html")
}, ex=function(){
    print("The 'PSCN' package is not available for R >= 3.0.0.")
    print("See http://cran.r-project.org/web/packages/PSCN/index.html")
})
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## HISTORY:
## 2014-02-13
## o Created from zzz.defunct/doPSCN.R.
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