R/imExposomeSet-toES.R

In rexposome: Exposome exploration and outcome data analysis

#' @describeIn imExposomeSet Returns an \code{\link{ExposomeSet}} with ethe given imputation.
setMethod(
    f = "toES",
    signature = "imExposomeSet",
    definition = function(object, rid=1) {
        if(rid > -1) {
            if(rid > object@nimputation) {
                stop("Given 'rid' with imputation number is too large.")
            }
            ee <- object@assayData[object@assayData$`.imp` == rid, -1, drop=FALSE]
            pp <- pData(object)[pData(object)$`.imp` == rid, -1, drop=FALSE]
              # object@phenoData[object@phenoData$`.imp` == rid, -1, drop=FALSE]

            rownames(ee) <- ee[ , 1]
            rownames(pp) <- pp[ , 1]
            loadExposome(
                exposures = as.data.frame(ee[ , -1]),
                #description = as.data.frame(object@featureData[ , -ncol(object@featureData)]),
                description = as.data.frame(fData(object)[ , -ncol(fData(object))]),
                phenotype = as.data.frame(pp[ , -1]),
                description.famCol = "Family"
            )
        } else {
            stop("'rid' sould be larger or equall to 1.")
        }
    }
)