R/Create_BED_files.R

In Uniquorn: Identification of cancer cell lines based on their weighted mutational/ variational fingerprint

#' create_bed_file
#' 
#' Creates BED files from the found and not found annotated mutations
#' 
#' @param match_t R table which contains the mutations from the 
#' training database for the cancer cell lines
#' @param vcf_fingerprint contains the mutations that are present 
#' in the query cancer cell line's vcf file
#' @param output_file Path to output file
#' @param ref_gen Reference genome version
#' @param manual_identifier Manually enter a vector of CL name(s) 
#' whose bed files should be created, independently from them 
#' passing the detection threshold
#' @return Returns a message which indicates if the BED file 
#' creation has succeeded
#' @usage 
#' create_bed_file(
#' match_t,
#' vcf_fingerprint,
#' output_file,
#' ref_gen,
#' manual_identifier
#' 
#' )
create_bed_file = function( 
    match_t,
    vcf_fingerprint,
    output_file,
    ref_gen,
    manual_identifier
){
    
    # prep
    
    # start
    
    print("Creating bed files")
    
    found_res_tab = res_table[ as.logical( res_table$Conf_score_sig ), ]
    found_identifier = paste(
        found_res_tab$CL, found_res_tab$CL_source, sep = "_"
    )
    
    found_identifier = unique( c( manual_identifier, found_identifier ) )
    
    for ( identifier in found_identifier ){
        
        if ( identifier != "" ){
            
            print(identifier)
            
            name_training_bed_file = stringr::str_replace(
                output_file,
                "_uniquorn_ident.tab",
                paste0( 
                    c(
                        "_uniquorn_ident_mutations_reference_variants_",
                        identifier,
                        ".bed"
                    ),
                    collapse = ""
                )
            )
            name_query_bed_file    = stringr::str_replace(
                output_file, "_uniquorn_ident.tab", 
                    paste0(
                        c(
                            "_uniquorn_ident_mutations_query_variants_",
                            identifier,
                            ".bed"
                        ),
                        collapse = ""
                    )
            )
            name_missed_bed_file = stringr::str_replace(
                output_file,
                "_uniquorn_ident.tab",
                paste0(
                    c(
                        "_uniquorn_ident_mutations_non_matching_variants_",
                        identifier,
                        ".bed"
                    ),
                    collapse = ""
                )
            )
            
            # training
            training_bed_file = paste0( 
                c( 
                    'track name=',
                    'Training_',
                    identifier,
                    ' description=Variants_in_reference type=bedDetail db=',
                    ref_gen,
                    ' color=0,0,255 priority=3'
                ),
                collapse = ""
            )
            
            training_coords = sim_list$Fingerprint[ sim_list$CL == identifier ]
            training_coords = stringr::str_trim( training_coords )
            training_coords = training_coords[
                !grepl("^[c(']", training_coords)]
            training_coords = stringr::str_split( training_coords, "_" )
            
            training_coords_res = sapply(training_coords, 
                FUN = function( vec ){ 
                    chrom = paste( "chr", stringr::str_trim(vec[1]), sep = "" )
                    return( 
                        paste0( 
                            c(
                                chrom,
                                as.character(
                                    as.integer(
                                        vec[2]
                                    ) - 1
                                ),
                                as.integer(
                                    as.integer(
                                        vec[3]
                                    )
                                )
                            ),
                            collapse = "\t"
                        )
                    )
                }
            )
            training_coords_res = c(
                training_bed_file,
                training_coords_res
            )
            
            utils::write.table( 
                x = training_coords_res,
                file =  name_training_bed_file,
                sep ="",
                row.names = FALSE,
                col.names = FALSE,
                quote = FALSE
            )
    
            # query
            
            query_bed_file = paste0( 
                c( 
                    'track name=',
                    'Query_',
                    identifier,
                    ' description=Variants_in_query type=bedDetail db=',
                    ref_gen,
                    ' color=0,255,0 priority=3'
                ),
                collapse = ""
            )
            
            query_coords = vcf_fingerprint
            query_coords = stringr::str_trim( query_coords )
            query_coords = query_coords[ ! grepl("^[c(']", query_coords ) ]
            query_coords = stringr::str_split( query_coords, "_" )
            
            query_coords_res = sapply( query_coords, FUN = function( vec ){ 
                chrom = paste( "chr", stringr::str_trim( vec[1] ), sep = "" )
                return( 
                    paste0(
                        c(
                            chrom,
                                as.character(
                                    as.integer(
                                        vec[2]
                                    ) - 1 
                                ),
                                as.integer(
                                    as.integer(
                                        vec[3]
                                    )
                                )
                        ),
                        collapse = "\t"
                    )
                )
            } )
            query_res = c( query_bed_file, query_coords_res )
            utils::write.table( 
                x = query_res,
                file =  name_query_bed_file,
                sep = "",
                row.names = FALSE,
                col.names = FALSE,
                quote     = FALSE 
            )        
                    
            # missed
            missed_bed_file = paste0( 
                c( 
                    'track name=',
                    'Missed_',
                    identifier,
                    ' description=Non_matching_variants type=bedDetail db=',
                    ref_gen,
                    ' color=255,0,0 priority=3'
                ),
                collapse = ""
            )
            
            missed_coords = training_coords[
                which( ! ( training_coords %in% query_coords ) ) ]
            
            missed_coords = sapply( missed_coords, FUN = function( vec ){ 
                chrom = paste( "chr", stringr::str_trim( vec[1] ), sep = "" )
                return(
                    paste0(
                        c(
                            chrom,
                                as.character(
                                    as.integer(
                                        vec[2]
                                    ) -1
                                ),
                                as.integer(
                                    as.integer(
                                        vec[3]
                                    )
                                )
                        ),
                        collapse = "\t"
                    )
                )
            })
            missed_coords_res = c( missed_bed_file, missed_coords )
            
            utils::write.table(
                x = missed_coords_res,
                file =  name_missed_bed_file,
                sep = "",
                row.names = FALSE,
                col.names = FALSE,
                quote = FALSE
            )
        }
    }
}