R/get_all_combinations.R

In DNABarcodeCompatibility: A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms

#' @title 
#' Get all compatible combinations.
#'
#' @description 
#' Finds the exhaustive set of compatible barcode combinations.
#'
#' @usage 
#' get_all_combinations(index_df, mplex_level, platform)
#'
#' @param index_df A dataframe containing barcodes identifiers, corresponding
#'  DNA sequences along with GC content and presence of homopolymers.
#' @param mplex_level The number at which the barcodes will be multiplexed.
#' Illumina recommends to not multiplex more than 96 libraries.
#' @param platform An integer representing the number of channels (1, 2, 4)
#' of the desired Illumina platform: 1 for iSeq; 2 for NextSeq, NovaSeq,
#' MiniSeq; 4 for HiSeq and MiSeq. 0 represents any other platform than
#' Illumina.
#'
#' @details 
#' Be aware that the total number of combinations may become prohibitively 
#' large for large barcode sets and large multiplexing numbers.
#'
#' @return 
#' A matrix containing the identifiers of compatible barcode combinations.
#'
#' @examples
#' get_all_combinations(DNABarcodeCompatibility::IlluminaIndexes, 2, 4)
#' 
#'
#' @seealso 
#' \code{\link{get_random_combinations}}
#' 
#' @export
#' 

get_all_combinations = function(index_df, mplex_level, platform){
    check_input_dataframe(  index_df, 
                            c("Id", "sequence", "GC_content", "homopolymer"))
    if (is.numeric(mplex_level)){
        if(mplex_level <= 96){
            if (mplex_level <= nrow(index_df)){
                combination_m = NULL
                if (platform == 4 ){
                    combinations_m = 
                        get_all_combinations_4_channel( index_df,
                                                        mplex_level)
                } else if (platform == 2){
                    combinations_m = 
                        get_all_combinations_2_channel( index_df, 
                                                        mplex_level)
                } else if (platform == 1){
                    combinations_m = 
                        get_all_combinations_1_channel( index_df, 
                                                        mplex_level)
                } else if (platform == 0){
                    combinations_m = 
                        get_all_combinations_0_channel( index_df, 
                                                        mplex_level)
                } else {
                    display_message("Please choose a correct platform 
                                        for your experiment ")
                }
                if(nrow(as.matrix(combinations_m)) == 0){
                    display_message(
                        paste(  "The programm didn't find any",
                                "compatible combination, please check", 
                                "your index list and your search",
                                "parameters"))
                    return (NULL)
                }else{
                    return (combinations_m)
                }
            } else {display_message(paste(  "The value of mplex_level",
                                            " should not be higher than the",
                                            "number of available barcodes"))
            }
        } else {display_message(
            "The value of mplex_level should not be higher than 96")
        }
    }else{
        display_message("Please enter a number as mplex_level")
        return(NULL)
    }
}