R/gtoxMthdList.R

In pmpsa-hpc/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.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# gtoxMthdList:
#-------------------------------------------------------------------------------

#' @rdname mthd_funcs
#' @export

gtoxMthdList <- function(lvl, type="mc") {

    tbl <- paste0(type, lvl, "_methods")
    qstring <- paste0("SELECT * FROM ", tbl, ";")

    ## Suppress warnings because the data fields are not recognized by R and
    ## imported as character.
    dat <- suppressWarnings(gtoxQuery(qstring, getOption("TCPL_DB")))

    if (nrow(dat) == 0) {
        warning("No ", type, lvl, " methods in the gtox databases.")
        return(dat[])
    }

    drop_cols <- c("created_date", "modified_date", "modified_by")
    dat <- dat[ , .SD, .SDcols=setdiff(names(dat), drop_cols)]

    dat[]

}

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