PromoterAnnotation-class
                        S4 class for promoter annotation data for a
                        specific annotation version
boxplotPromoters        Visualizes promoter activity and gene
                        expression with boxplots
calculateJunctionReadCounts
                        Calculate the total number of junction reads
                        overlapping with the introns of each promoter
                        for the input junction file
calculatePromoterReadCounts
                        Calculate the promoter read counts using
                        junction read counts approach for all the input
                        junction files
getAbsolutePromoterActivity
                        Prepare the absolute promoter activity table
                        including the promoter and gene ids
getAlternativePromoters
                        Identifies alternative promoters.
getGeneExpression       Prepare the gene expression table including the
                        gene ids
getRelativePromoterActivity
                        Prepare the relative promoter activity table
                        including the promoter and gene ids
integrateProactiv       Integrate multiple proActiv runs
normalizePromoterReadCounts
                        Normalize promoter read counts using DESeq2
plotHeatmap             Visualizes heatmap of features for samples
plotPCA                 Performs principal component analysis
preparePromoterAnnotation
                        Prepares promoter annotation from a gtf or txdb
proActiv                Estimates promoter counts and activity in a
                        single command
promoterAnnotation.gencode.v34.subset
                        Promoter annotation for Gencode.v34 (subset)
