R/do.combine.cols.R

In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis.

#' do.combine.cols - Combine the values of two columns into a single column
#'
#' This function allows you to combine the values of two columns, with an option to remove any 'NA' values
#'
#' @usage do.combine.cols(dat, col1, col2, na.rm)
#'
#' @param dat NO DEFAULT. Data.table.
#' @param col1 NO DEFAULT. Name of the column you want to combine into.
#' @param col2 NO DEFAULT. Name of the column you want to combine from. This column will be deleted after combination into col1.
#' @param na.rm DEFAULT = TRUE. If NA values are present in the columns, they will be removed.
#' 
#' @return Returns a data.table with adjusted columns
#'
#' @author Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au}
#'
#' @export

do.combine.cols <- function(dat, col1, col2, na.rm = TRUE){
      
  ### NA checks  
      
      na.checks <- rowSums(is.na(dat[,c(col1, col2), with = FALSE]))
      
      if(any(na.checks < 1)){
        stop("Less that one 'NA' per row")
      }
      
  ### Check class of col1
  
      cls <- class(dat[[col1]])
  
  ### Column combination
      
      if(isTRUE(na.rm)){
        dat[[col1]][is.na(dat[[col1]])] <- 'PLACEHOLDER'
        dat[[col2]][is.na(dat[[col2]])] <- 'PLACEHOLDER'
        dat[[col1]] <- paste0(dat[[col1]], dat[[col2]])
        dat[[col1]] <- gsub('PLACEHOLDER', '', dat[[col1]])
        dat[[col2]] <- NULL
      } else {
        dat[[col1]] <- paste0(dat[[col1]], dat[[col2]])
        dat[[col2]] <- NULL
      }

  ### Class adjust
      
      class(dat[[col1]]) <- cls
  
  ### Return
  
      return(dat)
  
}