R/doCBS.R

In mpierrejean/jointSeg: Joint Segmentation of Multivariate (Copy Number) Signals

#' Run CBS segmentation
#'
#' This function is a wrapper for convenient use of the \code{CBS} segmentation
#' method by \code{\link{PSSeg}}.  It applies the
#' \code{\link[DNAcopy]{segment}} function and reshapes the results
#'
#' @param y A numeric vector, the signal to be segmented
#' @param \dots Arguments to be passed to \code{\link[DNAcopy]{segment}}
#' @param verbose A \code{logical} value: should extra information be output ?
#' Defaults to \code{FALSE}.
#' @return A list with a single element: \describe{ \item{bkp}{breakpoint positions }}
#' @author Morgane Pierre-Jean and Pierre Neuvial
#' @seealso \code{\link[DNAcopy]{segment}}
#' @examples
#' ## load known real copy number regions
#' affyDat <- acnr::loadCnRegionData(dataSet="GSE29172", tumorFraction=1)
#'
#' ## generate a synthetic CN profile
#' K <- 10
#' len <- 1e4
#' sim <- getCopyNumberDataByResampling(len, K, minLength=100, regData=affyDat)
#' datS <- sim$profile
#'
#' ## run CBS segmentation
#' res <- doCBS(datS[["c"]])
#' getTpFp(res$bkp, sim$bkp, tol=5, relax = -1)   ## true and false positives
#' plotSeg(datS, breakpoints=list(sim$bkp, res$bkp))
#' @export doCBS
doCBS <- function(y, ..., verbose=FALSE) {
    if (!is.null(dim(y))) {
        if (ncol(y)==1 && mode(y)!="numeric"){
            y <- y[[1]]
            if (verbose) {
                print("Coercing 'y' to a vector")
            }
        } else {
            stop("Argument 'y' should be a numeric vector or a one column matrix/data frame")
        }

    }

    n <- length(y)
    chrom <- rep(1, n)
    maploc <- 1:n
    genomdat <- y
    cna <- DNAcopy::CNA(genomdat, chrom, maploc)
    res <- DNAcopy::segment(cna)

    bkp <- res$output$loc.end[-length(res$output$loc.end)]
    list(bkp=bkp)
}

############################################################################
## HISTORY:
## 2013-12-09
## o Renamed to 'doCBS'.
## 2013-05-16
## o Example code now embedded in a 'require()' statement to avoid
##   problems in the R CMD check mechanism of R-forge.
## 2013-01-09
## o Replaced 'jump' by 'bkp'.
## 2013-01-04
## o Created from 'segmentByCghseg'.
############################################################################