R/doPSCBS.R

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

doPSCBS <- structure(function(#Run Paired PSCBS segmentation
### This function is a wrapper for convenient use of the \code{PSCBS}
### segmentation method by \code{\link{PSSeg}}.  It applies the
### \code{\link[PSCBS]{segmentByPairedPSCBS}} function and reshapes the results
                              Y,
### A matrix of signals to be segmented, containing the
### following columns \describe{
### \item{c}{total copy numbers}
### \item{b}{allele B fractions (a.k.a. BAF)}
### \item{genotype}{germline genotypes}
### }
                              ...,
### Arguments to be passed to \code{\link[PSCBS]{segmentByPairedPSCBS}}
                              verbose=FALSE
### A \code{logical} value: should extra information be output ? Defaults to \code{FALSE}.
                              ) {
    ##seealso<<\code{\link[PSCBS]{segmentByPairedPSCBS}}
    
    if (!require("PSCBS")) {
        cat("Please install the 'PSCBS' package to run the 'doPSCBS' function")
        return()
    }
    if (is.null(dim(Y)) || is.data.frame(Y)) {
        if (verbose) {
            print("Coercing 'Y' to a matrix")
        }
        Y <- as.matrix(Y)
    } else if (!is.matrix(Y)){
        stop("Argument 'Y' should be a matrix, vector or data.frame")
    }

    cn <- colnames(Y)
    ecn <- c("c", "b", "genotype") ## expected
    mm <- match(ecn, cn)
    if (any(is.na(mm))) {
        str <- sprintf("('%s')", paste(ecn, collapse="','"))
        stop("Argument 'Y' should contain columns named ", str)
    }
    
    n <- as.numeric(nrow(Y))
    p <- dim(Y)[2]
    chrom <- rep(1, n)
    x <- 1:n
    genomdat <- cbind(CT=Y[, "c"], betaT=Y[, "b"], muN=Y[, "genotype"])
    data <- data.frame(genomdat, x=x)
    str(data)
    fit <- PSCBS::segmentByPairedPSCBS(data, tbn=FALSE) ##tbn=FALSE permits to use 'muN' and not 'betaN'
    res <- PSCBS::getSegments(fit, simplify=TRUE)
    bkp <- round(res$start[-1],0)
    res <- list(bkp=bkp) 
    return(res)
###  \item{bkp}{breakpoint positions}
}, ex=function(){
    if (require("PSCBS") && require("aroma.light")) {
        ## load known real copy number regions
        affyDat <- 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 PSCBS segmentation
        Y <- as.matrix(subset(datS, select=c(c, b, genotype)))
        res <- doPSCBS(Y)
        getTpFp(res$bkp, sim$bkp, tol=5, relax = -1)   ## true and false positives
        plotSeg(datS, breakpoints=list(sim$bkp, res$bkp))
    }
})

############################################################################
## HISTORY:
## 2013-12-09
## o Renamed to 'doPSCBS'
## 2013-05-30
## o Now explicitly requiring "aroma.light" as well.
## 2013-05-16
## o Example code now embedded in a 'require()' statement to avoid
##   problems in the R CMD check mechanism of R-forge.
## 2013-02-18
## o Bug fix.
## 2013-01-09
## o Replaced 'jump' by 'bkp'.
## 2013-01-04
## o Created from 'segmentByCBS'.
############################################################################