R/exposures_pData.R

In isglobal-brge/dsExposome: DataSHIELD server site Exposome functions

#' @title Exposures and phenotyphes data
#' 
#' @description Extract a table with the exposures and phenotypes data for all the individuals of an
#' Exposome Set
#'
#' @param exposomeSet  \code{ExposomeSet} Exposome Set object
#' @param target \code{character} To specify target of output table, \code{all} to include exposures and phenotypes,
#' \code{exposures} to include only the exposures and \code{phenotypes} to include only the phenotypes. Default \code{all}
#' @param exposures_type \code{character} Type of the exposures to be kept, usually 
#' \code{"numeric"} or \code{"character"/"factor"}. If \code{NULL} all the exposures will be kept.
#'
#' @return \code{data.frame} With exposures and phenotypes
#' @export

exposures_pData <- function(exposomeSet, target = "all", rownames2col = FALSE, exposures_type = NULL) {

  if(target == "all"){
    data <- cbind(rexposome::expos(exposomeSet), Biobase::pData(exposomeSet))
  }
  else if(target == "exposures"){
    if(!is.null(exposures_type)){
      select <- rownames(Biobase::fData(exposomeSet))[Biobase::fData(exposomeSet)$`.type` == exposures_type]
      data <- rexposome::expos(exposomeSet)[ , select]
    } else {
      data <- rexposome::expos(exposomeSet)
    }
  }
  else if(target == "phenotypes"){
    data <- Biobase::pData(exposomeSet)
  }
  
  else{stop("Incorrect 'target' argument. Options: 'all', 'exposures' and 'phenotypes'", call.=FALSE)}
  
  if(rownames2col){
    data %>% tibble::rownames_to_column("id") -> data
  }
  
  return(data)

}