R/hellingerDist.R

In guigolab/sQTLseekeR2: R package for splicing QTL mapping

##' Computes Hellinger distance for each pair of columns from the input
##' data.
##' @title Hellinger distance computation
##' @param sr a matrix or data.frame with the transcript relative
##' expression for each sample (column).
##' @return a matrix with the pairwise distance between samples.
##' @author Jean Monlong
##' @keywords internal
hellingerDist <- function(sr)
{
    k <- dim(sr)[2]
    interdist <- matrix(data = 0, nrow = k, ncol = k)
    for(i in 1:k) {
        for(j in 1:i) {
                interdist[i, j] <- hellingerDist.p(sr[, i], sr[, j])          
        }
    }
    interdist <- interdist + t(interdist)
    colnames(interdist) <- rownames(interdist) <- colnames(sr)
    non.na <- !is.na(diag(interdist))                           
    interdist <- interdist[non.na, non.na]
    return(stats::as.dist(interdist))
}

hellingerDist.p <- function(x1, x2)
{
    a <- (sqrt(x1) - sqrt(x2))
    b <- sqrt(sum(a * a))
    return(b)
}