R/ExposomeSet-highAndLow.R

In isglobal-brge/rexposome: Exposome exploration and outcome data analysis

#' @describeIn ExposomeSet Performs a discretization of continuous exposures.
#' @param ngroups Number of intervals to be used
#' @param intervals If \code{"standard"} all levels are kept, if
#' \code{"extreme"} intermetiate levels are set to \code{NA}.
#' @param select Vector selecting thee xposures to be used.
#' @param drop If set to \code{TRUE} exposures are replaced
setMethod(
    f = "highAndLow",
    signature = "ExposomeSet",
    definition = function(object, ngroups = 3,
                          intervals = c("standard", "extreme"), select,
                          drop = FALSE, warnings = TRUE) {
        intervals <- match.arg(intervals)
        if (warnings) {
            warning("Non continuous exposures will be keept but not transformed")
        }
        if(ngroups < 2) {
            stop("Invalid argument 'ngroups'. It must be equal or greather than 2")
        }

        ## SELECT NUMERICAL EXPOSURES
        if(missing(select)) {
            select.all <- fData(object)[ , ".type"]
            names(select.all) <- exposureNames(object)
            select <- names(select.all[select.all == "numeric"])
        } else {
            select.all <- fData(object)[ , ".type"]
            names(select.all) <- exposureNames(object)
            if(sum(select.all[select] == "numeric") != length(select)) {
                stop("Exposures in 'select' are not numerical.")
            }
        }
        ## /

        ## COVNERT FROM CNT TO DST
        data.cnt <- expos(object)[, select, drop=FALSE]
        data.dst <- data.frame(lapply(colnames(data.cnt), function(exp) {
            gtools::quantcut(data.cnt[ , exp], seq(0, 1, length = ngroups + 1),
                             right = FALSE)
        }))
        ##

        ## IF EXTREM PLACE NA TO MIDLE GROUPS
        if(intervals == "extreme") {
            lapply(colnames(data.dst), function(exp) {
                lvl <- levels(data.dst[ , exp])
                data.dst[!(data.dst[ , exp] %in% c(max(lvl), min(lvl))) , exp] <- NA
            })
            trs <- "EXT"
        } else {
            trs <- "HaL"
        }
        ## /

        if(drop) {
            select.all <- names(select.all)
            select.no <- select.all[!select.all %in% select]
            data.dst <- cbind(data.dst,
                              t(assayData(object)[["exp"]][select.no, ]))
            colnames(data.dst) <- c(select, select.no)
            data.dst <- data.dst[ , rownames(assayDataElement(object, "exp"))]
            assayData(object) <- assayDataNew("environment",
                exp = t(data.dst))

            nfData <- fData(object)
            nfData[select, ".type"] <- "factor"
            nfData[select, ".fct"] <- trs
            fData(object) <- nfData

        } else {

            ## PLACE NEW NAMES TO EXPOSURES
            colnames(data.dst) <- paste(select, ".HL", sep = "")
            rownames(data.dst) <- rownames(data.cnt)
            ## /

            assayData(object) <- assayDataNew("environment",
                  exp = rbind(assayDataElement(object, "exp"), t(data.dst))
            )

            nfData <- fData(object)[select, ]
            rownames(nfData) <- colnames(data.dst)
            nfData[ , ".type"] <- "factor"
            nfData[ , ".fct"] <- trs
            fData(object) <- rbind(fData(object), nfData)
        }
        object
    }
)