R/normalizeAverage.R

In cn.farms: cn.FARMS - factor analysis for copy number estimation

#' Scales the range of the non-polymorphic data to the range of a given array.
#' @param x Data matrix
#' @param baselineArray Choose the baseline channel array.
#' @param avg The function for averaging.
#' @param targetAvg Value to which the array should be averaged.
#' @param ... Further optional parameters.
#' @return Normalized non-polymorphic data.
#' @author Djork-Arne Clevert \email{okko@@clevert.de} and 
#' Andreas Mitterecker \email{mitterecker@@bioinf.jku.at}
#' @export 
#' @examples
#' x <- matrix(rnorm(100, 11), 20, 5)
#' normalizeAverage(x, x[, 1])
normalizeAverage <- function(x, baselineArray, avg = median, 
        targetAvg = 2200, ...) {
    
    if (missing(baselineArray)) {
        baselineArray <- x[, 1:2, drop = FALSE]
    }
    
    ## Estimate the scale for each channel
    scale <- apply(x, MARGIN = 2, FUN = avg, ...)
    
    ##FIXME: 
    #scale1 <- apply(x, MARGIN = 2, FUN = avg, ...)
    scale1 <- median(baselineArray)
    targetAvg <- 2200
    
    ## Standardize so that the 'baseline' channel has scale one.
    scale <- scale / scale1
    
    ## Rescale to target averages?
    if (!is.null(targetAvg)) {
        rho <- (scale1 / targetAvg)
        scale <- rho * scale
    }
    
    ## Rescale so that all channels have the same scale
    for (cc in 1:ncol(x)) {
        x[, cc] <- x[, cc] / scale[cc]
    }
    
    return(x)
}