R/SanityCheck.R

In ToxicoGx: Analysis of Large-Scale Toxico-Genomic Data

sanitizeInput <- function(conc,
                          viability,
                          Hill_fit,
                          conc_as_log = FALSE,
                          viability_as_pct = TRUE,
                          trunc = TRUE,
                          verbose = TRUE) # Set to 2 to see debug messageouts
  {

  if (is.logical(conc_as_log) == FALSE) {
    message(conc_as_log)
    stop("'conc_as_log' is not a logical.")
  }

  if (is.logical(viability_as_pct) == FALSE) {
    message(viability_as_pct)
    stop("'viability_as_pct' is not a logical.")
  }

  if (is.logical(trunc) == FALSE) {
    message(trunc)
    stop("'trunc' is not a logical.")
  }
  if(!is.finite(verbose)){
    stop("'verbose' should be a logical (or numerical) argument.")
  }
  if(!missing(viability)&&!missing(conc)&&missing(Hill_fit))
  {
    if (length(conc) != length(viability)) {
      if(verbose==2){
        message(conc)
        message(viability)
      }
      stop("Log concentration vector is not of same length as viability vector.")
    }
    if( any(is.na(conc)&(!is.na(viability)))){
      warning("Missing concentrations with non-missing viability values encountered. Removing viability values correspoding to those concentrations")

      myx <- !is.na(conc)
      conc <- as.numeric(conc[myx])
      viability <- as.numeric(viability[myx])

    }
    if(any((!is.na(conc))&is.na(viability))){

      warning("Missing viability with non-missing concentrations values encountered. Removing concentrations values correspoding to those viabilities")
      myx <- !is.na(viability)
      conc <- as.numeric(conc[myx])
      viability <- as.numeric(viability[myx])

    }
    conc <- as.numeric(conc[!is.na(conc)])
    viability <- as.numeric(viability[!is.na(viability)])

    #CHECK THAT FUNCTION INPUTS ARE APPROPRIATE
    if (prod(is.finite(conc)) != 1) {
      message(conc)
      stop("Concentration vector contains elements which are not real numbers.")
    }

    if (prod(is.finite(viability)) != 1) {
      message(viability)
      stop("Viability vector contains elements which are not real numbers.")
    }


    if (min(viability) < 0) {
      if (verbose) {

        warning("Warning: Negative viability data.")
      }
    }

    if (max(viability) > (1 + 99 * viability_as_pct)) {
      if (verbose) {
        warning("Warning: Viability data exceeds negative control.")
      }
    }


    if (conc_as_log == FALSE && min(conc) < 0) {
      if (verbose == 2) {
        message(conc)
        message(conc_as_log)
      }
      stop("Negative concentrations encountered. Concentration data may be inappropriate, or 'conc_as_log' flag may be set incorrectly.")
    }

    if (viability_as_pct == TRUE && max(viability) < 5) {
      warning("Warning: 'viability_as_pct' flag may be set incorrectly.")
      if (verbose == 2) {

        message(viability)
        message(viability_as_pct)
      }
    }

    if (viability_as_pct == FALSE && max(viability) > 5) {
      warning("Warning: 'viability_as_pct' flag may be set incorrectly.")
      if (verbose == 2) {
        message(viability)
        message(viability_as_pct)
      }
    }

    if(is.unsorted(conc)){
      warning("Concentration Values were unsorted. Sorting concentration and ordering viability in same order")
      myx <- order(conc)
      conc <- conc[myx]
      viability <- viability[myx]
    }

    #CONVERT DOSE-RESPONSE DATA TO APPROPRIATE INTERNAL REPRESENTATION
    if (conc_as_log == FALSE ) {
      ii <- which(conc == 0)
      if(length(ii) > 0) {
        conc <- conc[-ii]
        viability <- viability[-ii]
      }

      log_conc <- log10(conc)
    } else {
      log_conc <- conc
    }

    if (viability_as_pct == TRUE) {
      viability <- viability / 100
    }
    if (trunc) {
      viability = pmin(as.numeric(viability), 1)
      viability = pmax(as.numeric(viability), 0)
    }

    return(list("log_conc"=log_conc, "viability"=viability))
  }
  if(!missing(Hill_fit) && missing(viability)){
    if(is.list(Hill_fit)){

      Hill_fit <- unlist(Hill_fit)
    }
    if (conc_as_log == FALSE && Hill_fit[[3]] < 0) {
      message("EC50 passed in as:")
      message(Hill_fit[[3]])
      stop("'conc_as_log' flag may be set incorrectly, as the EC50 is negative when positive value is expected.")
    }


    if (viability_as_pct == FALSE && Hill_fit[[2]] > 1) {
      message("Einf passed in as:")
      message(Hill_fit[[2]])

      warning("Warning: 'viability_as_pct' flag may be set incorrectly.")

    }
    if (conc_as_log == FALSE){
      Hill_fit[[3]] <- log10(Hill_fit[[3]])
    }
    if (viability_as_pct == TRUE){
      Hill_fit[[2]] <- Hill_fit[[2]]/100
    }
    if(missing(conc)){
      return(list("Hill_fit"=Hill_fit))
    } else {
      conc <- as.numeric(conc[!is.na(conc)])

      if (prod(is.finite(conc)) != 1) {
        message(conc)
        stop("Concentration vector contains elements which are not real numbers.")
      }
      if (conc_as_log == FALSE && min(conc) < 0) {
        message(conc)
        message(conc_as_log)
        stop("Negative concentrations encountered. Concentration data may be inappropriate, or 'conc_as_log' flag may be set incorrectly.")
      }

      if (conc_as_log == FALSE ) {
        ii <- which(conc == 0)
        if(length(ii) > 0) {
          conc <- conc[-ii]
        }
        log_conc <- log10(conc)
      } else {
        log_conc <- conc
      }
      if(is.unsorted(conc)){
        myx <- order(conc)
        conc <- conc[myx]
      }
      return(list("Hill_fit"=Hill_fit, "log_conc" = log_conc))
    }


  }
  if(!missing(Hill_fit)&&!missing(viability)){

    stop("Please pass in only one of 'Hill_fit' and 'viability', it is unclear which to use in the computation.")
  }
  if(missing(Hill_fit)&&missing(viability)){

    stop("Both 'Hill_fit' and 'viability' missing, please pass in some data!")
  }
}