R/gtoxPrepOtpt.R

In philipmorrisintl/GladiaTOX: R Package for Processing High Content Screening data

#####################################################################
## This program is distributed in the hope that it will be useful, ##
## but WITHOUT ANY WARRANTY; without even the implied warranty of  ##
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the    ##
## GNU General Public License for more details.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# gtoxPrepOtpt: Map assay/chemcial ID values to names
#-------------------------------------------------------------------------------

#' @title Map assay/chemcial ID values to annotation information
#'
#' @description
#' \code{gtoxPrepOtpt} queries the chemical and assay information from the gtox
#' database, and maps the annotation information to the given data.
#'
#' @param dat data.table, output from \code{\link{gtoxLoadData}}
#' @param ids Character, (optional) a subset of ID fields to map
#'
#' @details
#' \code{gtoxPrepOtpt} is used to map chemical and assay identifiers to their
#' respective names and annotation information to create a human-readable table
#' that is more suitable for an export/output.
#'
#' By default the function will map sample ID (spid), assay component id (acid),
#' and assay endpoint ID (aeid) values. However, if 'ids' is not null, the
#' function will only attempt to map the ID fields given by 'ids.'
#'
#' @examples
#' ## Store the current config settings, so they can be reloaded at the end
#' ## of the examples
#' conf_store <- gtoxConfList()
#' gtoxConfDefault()
#'
#' ## Load some example data
#' d1 <- gtoxLoadData(1)
#'
#' ## Check for chemical name in 'dat'
#' "chnm" %in% names(d1) ## FALSE
#'
#' ## Map chemical annotation only
#' d2 <- gtoxPrepOtpt(d1, ids = "spid")
#' "chnm" %in% names(d2) ## TRUE
#' "acnm" %in% names(d2) ## FALSE
#'
#' ## Map all annotations
#' d3 <- gtoxPrepOtpt(d1) ## Also works if function is given d2
#' "chnm" %in% names(d2) ## TRUE
#' "acnm" %in% names(d2) ## FALSE
#' 
#' ## Reset configuration
#' options(conf_store)
#'
#' @return The given data.table with chemical and assay information mapped
#' @export

gtoxPrepOtpt <- function(dat, ids=NULL) {

    ## Variable-binding to pass R CMD Check
    acnm <- acid <- aenm <- resp_unit <- aeid <- spid <- chid <- NULL
    code <- chnm <- casn <- NULL

    if (!"data.table" %in% class(dat)) {
        stop("'dat' must be a data.table.")
    }

    dnames <- names(dat)

    if (is.null(ids)) ids <- dnames

    if ("acid" %in% ids) { # Map acid names
        if (!"acid" %in% dnames) {
            warning("'acid' field is not in dat. No 'acid' mapping performed.")
        } else {
            if ("acnm" %in% dnames) dat[ , acnm := NULL]
            dat <- merge(
                x=gtoxLoadAcid("acid", dat[ , unique(acid)]),
                y=dat,
                by="acid",
                all.y=TRUE
            )
        }
    }

    if ("aeid" %in% ids) { # Map aeid names and resp_units
        if (!"aeid" %in% dnames) {
            warning("'aeid' field is not in dat. No 'aeid' mapping performed.")
        } else {
            if ("aenm" %in% dnames) dat[ , aenm := NULL]
            if ("resp_unit" %in% dnames) dat[ , resp_unit := NULL]
            dat <- merge(
                x=gtoxLoadAeid("aeid", dat[ , unique(aeid)]),
                y=dat,
                by="aeid",
                all.y=TRUE
            )
            dat <- merge(dat, gtoxLoadUnit(dat[ , unique(aeid)]), by="aeid")
        }
    }

    if ("spid" %in% ids) {
        if (!"spid" %in% dnames) {
            warning("'spid' field is not in dat. No 'spid' mapping performed.")
        } else {
            if ("chid" %in% dnames) dat[ , chid := NULL]
            if ("casn" %in% dnames) dat[ , casn := NULL]
            if ("chnm" %in% dnames) dat[ , chnm := NULL]
            if ("code" %in% dnames) dat[ , code := NULL]
            cmap <- suppressWarnings(gtoxLoadChem("spid", dat[ , unique(spid)]))
            dat <- merge(cmap, dat, by="spid", all.y=TRUE)
        }
    }

    dat[]

}

#-------------------------------------------------------------------------------