R/filterWith.R

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

#' S4 method to filter a dataElement
#'
#' @param da first dataElement
#' @param fi the filter
#' @return the reordered dataElement
#'
#' @export
setGeneric("filterWith", function(da, fi) {
  standardGeneric("filterWith")
})

#' S4 method to filter a dataElement
#'
#' @param da first dataElement
#' @param fi the filter
#' @return the reordered dataElement
#'
#' @export
setMethod("filterWith",
          c(da = "dataElement", fi = "logical"),
          function(da, fi) {
            if (length(fi) == nrow(da@obsDescr[[1]])) {
              if (da@type != "ANN") {
                da <- setDataPart(da, getDataPart(da)[fi,, drop = FALSE])
              }
              for (i in 1:length(da@obsDescr)) {
                da@obsDescr[[i]] <- da@obsDescr[[i]][fi,, drop = FALSE]
              }
              return(da)
            } else {
              stop(crayon::red("fusion::filterWith >> length(fi) != nrow(da)"))
            }
          }
)