R/indexTransform.R

In mdgsa: Multi Dimensional Gene Set Analysis.

##indexTransform.r
##2013-03-25 dmontaner@cipf.es

index.standardize <- function (index) {
    m <- mean (index, na.rm = TRUE)
    s <- sd   (index, na.rm = TRUE)
    index <- (index - m) / s
    index
}

index.normalize <- function (index) {
    ##Standardize to normal distribution (quantiles of a normal distribution

    ##check that index is numeric
    if (!is.numeric (index)) stop ("index is not numeric")  
    
    res <- qqnorm (index, plot.it = FALSE)$x
    if (!is.null (names (index))){
        names (res) <- names (index)
    }
    res
}

################################################################################

##' @name indexTransform
## @docType 
##' @author David Montaner \email{dmontaner@@cipf.es}
##' 
## @aliases 
##' 
##' @keywords transform ranking index
##' @seealso \code{\link{transferIndex}}, \code{\link{uvGsa}},
##' \code{\link{mdPat}}
##'
##' @title Transform ranking index distribution.
##' 
##' @description
##' The function performs a transformation of the ranking index so that
##' its distribution is suitable as independent variable of the
##' logistic regression model.
##' 
##' @details
##' Works for vector, matrices and data.frames.
##' In the case of matrices the function transforms each column separately
##' from the other ones.
##'
##' Two methods are currently implemented:
##' \describe{
##'   \item{- normalize:}{transforms the index into quantiles of a normal distribution.}
##'   \item{- standardize:}{performs an statistical standardization by subtracting
##'   the mean and dividing by the standard deviation.}
##' }
##'
##' @param index a ranking index; a numeric vector, matrix or data.frame.
##' @param method transformation method. See details.
##' 
##' @return A transformed index. Its class will be that of the the input object.
##'
##' @examples
##' myIndex <- runif (1000)
##' myTransformedIndex <- indexTransform (myIndex)
##' plot (myIndex, myTransformedIndex)
##' 
##' @export
##' 
indexTransform <- function (index, method = "normalize") {
  
    metodos <- c("normalize", "standardize", "none")
    if (!method %in% metodos) {
        stop (paste ("method should be one of:",
                     paste (metodos, collapse = ", ")))
    }
    
    if (method == "normalize") {
        if (is.matrix (index) | is.data.frame (index)) {
            index <- apply (index, 2, index.normalize)
        } else {
            index <- index.normalize (index)
        }
    }
    
    if (method == "standardize") {
        if (is.matrix (index) | is.data.frame (index)) {
            index <- apply (index, 2, index.standardize)
        } else {
            index <- index.standardize (index)
        }
    }
    
    ## if (method == "none") {
    ##   no change
    ## }
    
    ## OUTPUT
    index
}