R/tpp2dCalcFractAbundance.R

In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

#' @title Calculate fractional abundance and DMSO ratio of successive sumionareas  
#'   (usage of function is only reasonable when at least two temperatures are multiplexed!)
#'   
#' @description Calculates fractional abundance and DMSO ratio of successive sumionareas and 
#'   creates respective columns which are added two the data frame which is handed over
#'  
#' @examples 
#' data(panobinostat_2DTPP_smallExample)
#' 
#' # Import data:
#' datIn <- tpp2dImport(configTable = panobinostat_2DTPP_config,
#'                       data = panobinostat_2DTPP_data,
#'                       idVar = "representative",
#'                       addCol = "clustername",
#'                       intensityStr = "sumionarea_protein_",
#'                       nonZeroCols = "qusm")
#'
#' # View attributes of imported data (experiment infos and import arguments):
#' attr(datIn, "importSettings") %>% unlist
#' attr(datIn, "configTable")
#' 
#' # Compute fractional abundance:
#' datDMSORatio <- tpp2dCalcFractAbundance(data = datIn)
#' colnames(datDMSORatio)
#' 
#' @param configTable DEPCRECATED
#' @param data data frame of TPP-CCR results (e.g. obtained by \code{run2DTPPCCR}).
#' @param intensityStr DEPCRECATED
#' @param idVar DEPCRECATED

#'  
#' @return Data frame that was handed over with additional columns of fractional abundance
#'   and DMSO1 vs DMSO2 ratio
#'   
#' @export
tpp2dCalcFractAbundance <- function(configTable = NULL, data, 
                                    intensityStr = NULL, 
                                    idVar = NULL){
  
  if (!missing(configTable)){
    warning("`configTable` is deprecated.", call. = TRUE)
  }
  
  if (!missing(intensityStr)){
    warning("`intensityStr` is deprecated.", call. = TRUE)
  }
  
  if (!missing(idVar)){
    warning("`idVar` is deprecated.", call. = TRUE)
  }
  
  # Check for missing function arguments
  checkFunctionArgs(match.call(), c("data"))
  
  message("Calculating fractional abundance and DMSO1 vs. DMSO2 ratio...")
  
  # Obtain config table used for data import (stored as attribute of imported data):
  configTable <- attr(data, "configTable")
  
  # Obtain settings used for data import (stored as attribute of imported data):
  importSettings <- attr(data, "importSettings")
  intensityStr <- importSettings$intensityStr
  idVar <- importSettings$proteinIdCol
  
  # determine adjacent temperature pairs
  compound <- as.character(configTable$Compound[1])
  all.temps <- configTable$Temperature
  temps.num <- length(all.temps)
  temp.pairs <- split(all.temps, as.factor(sort(rank(all.temps)%%(temps.num/2))))
  intensity.cols <- grep(intensityStr, colnames(data))
  # loop over all proteins and calculate fractional abundance for each adjacent temperature pair
  subset.list <- lapply(unique(data[[idVar]]), function(prot){
    # subset data according to only one protein
    CCR.subset <- data[which(data[[idVar]] == prot),]
    if (nrow(CCR.subset) == temps.num){
      # loop over all temp pairs and calc DMSO1/DMSO2
      temp.ratios <- sapply(temp.pairs, function(t.pair){
        row1 <- grep(as.character(t.pair[1]), CCR.subset[["temperature"]])
        row2 <- grep(as.character(t.pair[2]), CCR.subset[["temperature"]])
        # calc dmso1 vs dmso2 
        dmso.ratio <- as.numeric(as.character(CCR.subset[row1, intensity.cols[length(intensity.cols)]]))/
          as.numeric(as.character(CCR.subset[row2, intensity.cols[length(intensity.cols)]]))
        # calc sumionarea1 vs sum(sumionareas1, sumionareas2)
        f.abund1 <- 100*sum(as.numeric(sapply(CCR.subset[row1, intensity.cols], as.character)))/
          sum(as.numeric(sapply(CCR.subset[row1, intensity.cols], as.character)), 
              as.numeric(sapply(CCR.subset[row2, intensity.cols], as.character)))
        # calc sumionarea2 vs sum(sumionareas1, sumionareas2)
        f.abund2 <- 100*sum(as.numeric(sapply(CCR.subset[row2, intensity.cols], as.character)))/
          sum(as.numeric(sapply(CCR.subset[row1, intensity.cols], as.character)), 
              as.numeric(sapply(CCR.subset[row2, intensity.cols], as.character)))
        return(list(dmso.ratio, f.abund1, f.abund2))
      })
      CCR.subset$dmso1_vs_dmso2 <- unlist(rep(temp.ratios[1,], each=2))
      CCR.subset$total_sumionarea_fraction <- as.vector(rbind(unlist(temp.ratios[2,]), 
                                                              unlist(temp.ratios[3,])))
    }else{
      CCR.subset$dmso1_vs_dmso2 <- rep(NA, nrow(CCR.subset))
      CCR.subset$total_sumionarea_fraction <- rep(NA, nrow(CCR.subset))
    }
    return(CCR.subset)
  })
  
  out <- do.call(rbind, subset.list)
  attr(out, "importSettings") <- importSettings
  attr(out, "configTable")    <- configTable
  
  return(out)
}