R/combine_data.R

In Dahaniel/DoOR.functions: Integrating Heterogeneous Odorant Response Data into a Common Response Model: A DoOR to the Complete Olfactome

# Combine Two Data Sets
#
# Combine two data sets into one byInChIKey
#
# Data frames are merged by InChIKey. Data2 will be merged into data1 specified
# by the column name \code{by.data2} into one. The name of added column could be
# assigned with \code{assigned.name}. If \code{data2} contains some odors that
# the \code{data1} do not have, then the new odors will be added into output.
#
# @param data1 data frame, the object to be added.
# @param data2 data frame, it will be merged to "data1".
# @param by.data2 character string, a column name in "data2", specify which
#   column will be combined into data1.
# @param assigned.name charater string, assigning a name to combined column.
# @author Shouwen Ma <\email{shouwen.ma@@uni-konstanz.de}>
# @author Daniel Münch <\email{daniel.muench@@uni-konstanz.de}>
# @keywords data
# @examples
#
# library(DoOR.data)
# library(DoOR.functions)
# newdata <- data.frame(InChIKey=odor$InChIKey[1:4],
# 	new.data=c(0.4, 0.5, 0.6, 0.7))
# data(Or22a)
# new.Or22a <- combine_data(data1 = Or22a, data2 = newdata,
#               by.data2 = "new.data")
#
combine_data <-
  function(data1,
           data2,
           by.data2,
           assigned.name,
           ident = door_default_values("ident"))
  {
    if (any(duplicated(data2[, ident])))
      stop('There are duplicated identifiers in the new dataset, please solve 
           this first.')
    new.odor <- which(is.na(match(data2[, ident], data1[, ident])))
    
    # if no new odor
    if (is.na(new.odor[1])) {
      output 	  <- data1
      matchOdor <- match(data2[, ident], output[, ident])
      if (missing(assigned.name))
        assigned.name <- by.data2
      output[matchOdor, assigned.name] <- data2[, by.data2]
    } else {
      data_NewOdor <- data2[new.odor, ]
      l.d1 <- length(data1[, ident])
      l.d2 <- length(data_NewOdor[, ident])
      nrow.new <- l.d1 + l.d2
      first_NewOdor <- data1[(l.d1 + 1), ]
      output <- data1
      
      # add new odors to the frame one by one
      for (i in seq(l.d2)) {
        next_NewOdor 	     <- first_NewOdor
        next_NewOdor[, ident] <- as.character(data_NewOdor[i, ident])
        output 		     <- rbind(output, next_NewOdor)
        rownames(output)     <- seq(l.d1 + i)
      }
      
      if (missing(assigned.name))
        assigned.name <- by.data2
      
      # add response values of new odors to the output one by one
      for (i in seq(l.d2)) {
        output[l.d1 + i, assigned.name] <- data_NewOdor[i, by.data2]
      }
      
      matchOdor <- match(data2[, ident], output[, ident])
      output[matchOdor, assigned.name] <- data2[, by.data2]
    }
    
    
    return(output)
  }