R/matchTo.R

In jwist/fusion: Fusion: Objects class definitions for metabolic profiling

#' function to match one dataElement against a second one
#'
#' @param daA first dataElement
#' @param daB second dataElement
#' @param using the name of the column used as UID
#' @return dataElement with matched samples
#'
#' @export
matchTo <- function(daA, daB, using = "sampleID") {

  if (is(daA, "dataElement") == is(daB, "dataElement")) {
    check(daA, using)
    check(daB, using)

    fi <- match(getID(daA, using), getID(daB, using))

    # check for diffs (NA)
    fn <- is.na(fi)
    if (sum(fn) > 0) {
      daA <- filterWith(daA, !fn)
    }

    if (sum(fn) != 0) {
      warning(paste("fusion::matchTo >>",
                    sum(fn) ,
                   "sample(s) dropped"))
    }

    # sort and order
    idx <- sort(fi, index.return = TRUE)$ix
    daA <- orderWith(daA, idx)

    return(daA)

  } else {
    stop("fusion: both objects to match
         must be of class dataElement")
  }
}