R/omitdiag.R

In lineup: Lining Up Two Sets of Measurements

## omitdiag.R
## Karl W Broman

#' Replace the diagonal in a distance matrix with missing values
#'
#' Replace the diagonal (that is, self-self distances) from a distance matrix
#' calculated by [distee()] or [disteg()] with missing
#' values (so that only self-nonself distances are left).
#'
#' We use the row and column names to identify which entries are self-self.
#'
#' @param d A distance matrix calculated by [distee()] or
#' [disteg()].
#' @return A matrix of the same form as the input, but with self-self distances
#' replaced with `NA`.
#' @author Karl W Broman, \email{broman@@wisc.edu}
#' @seealso [pulldiag()], [distee()], [disteg()],
#' [summary.lineupdist()], [plot2dist()],
#' [plot.lineupdist()]
#' @keywords array
#' @examples
#' data(expr1, expr2)
#'
#' \dontshow{expr1 <- expr1[,1:500]
#' expr2 <- expr2[,1:500]}
#'
#' # distance as RMS difference
#' d <- distee(expr1, expr2)
#'
#' # focus on the self-nonself distances
#' # (replace self-self distances with NA)
#' d_selfnonself <- omitdiag(d)
#'
#' @export
omitdiag <-
    function(d)
{
    rn <- rownames(d)
    cn <- colnames(d)
    m <- match(rn, cn)
    wh <- which(!is.na(m))
    m <- m[!is.na(m)]
    for(i in seq(along=wh))
        d[wh[i],m[i]] <- NA

    d
}