R/spikePipe-methods.R

In ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

spikePipe <- function(infoFile, bamPath, bigWigPath, anno, genome_version, 
                paired = FALSE, binsize = 50, profile_length_before = 2000, 
                profile_length_after= 2000, mean_or_median = "mean", 
                interpolation_number = 100, interpolation_average = 10000,
                ignore_strand = FALSE, verbose = FALSE, boost = FALSE, 
                outputFolder = NULL){
            
            if(.Platform$OS.type != 'windows') {
                csds <- spikeDataset(infoFile, bamPath, bigWigPath, boost, 
                        verbose)
                
                if(verbose)
                    message("\n\n\t\t ### Step 1. Computing scaling factors ",
                            "###")
                
                csds <- estimateScalingFactors(csds, paired, verbose)
                
                if(verbose)
                    message("\n\n\t\t ### Step 2. RPM scaling ###")
                
                csds <- scaling(csds, verbose = verbose, 
                        outputFolder = outputFolder)
                
                if(verbose)
                    message("\n\n\t\t ### Step 3. Input Subtraction ###")
                
                csds <- inputSubtraction(csds, verbose)
                
                if(verbose)
                    message("\n\n\t\t ### Step 4. Reverse RPM scaling ###")
                
                csds <- scaling(csds, reverse = TRUE, verbose = verbose)
                
                if(verbose)
                    message("\n\n\t\t ### Step 5. Spike-in scaling ###")
                
                csds <- scaling(csds, type = "exo", verbose = verbose)
                
                if(boost){
                    if(verbose)
                        message("\n\n\t\t ### Step 6. Writing spiked files ",
                                "###")
                    
                    exportBigWigs(csds, verbose)
                }
                
                if(boost){
                    if(verbose)
                        message("\n\n\t\t ### Step 7. Extract values ###")
                }else{
                    if(verbose)
                        message("\n\n\t\t ### Step 6. Extract values ###")
                }
                
                csds <- extractBinding(csds, anno, genome_version, binsize, 
                        profile_length_before, profile_length_after, 
                        mean_or_median, interpolation_number, 
                        interpolation_average, ignore_strand, verbose)
                
                return(csds)
            }else{
                stop("As of rtracklayer >= 1.37.6, BigWig is not ",
                        "supported on Windows.")
            }
        }