SGFeatureCounts         Constructor function for S4 class
                        'SGFeatureCounts'
SGFeatures              Constructor function for S4 class 'SGFeatures'
SGVariantCounts         Constructor function for S4 class
                        'SGFeatureCounts'
SGVariants              Constructor function for S4 class 'SGVariants'
TxFeatures              Constructor function for S4 class 'TxFeatures'
analyzeFeatures         Analysis of splice graph features from BAM
                        files
analyzeVariants         Analysis of splice variants
annotate                Annotation with respect to transcript features
assays                  Accessing and replacing assay data
convertToSGFeatures     Convert transcript features to splice graph
                        features
convertToTxFeatures     Convert to TxFeatures object
exportFeatures          Export to BED format
findSGVariants          Find splice variants from splice graph
getBamInfo              Obtain library information from BAM files
getSGFeatureCounts      Compatible counts for splice graph features
                        from BAM files
getSGVariantCounts      Representative counts and frequency estimates
                        for splice variants
makeSGFeatureCounts     Create 'SGFeatureCounts' object
mergeTxFeatures         Merge redundant features
plotFeatures            Plot splice graph and heatmap of expression
                        values
plotSpliceGraph         Plot splice graph
plotVariants            Plot splice graph and heatmap of splice variant
                        frequencies
predictTxFeatures       Splice junction and exon prediction from BAM
                        files
processTerminalExons    Process predicted terminal exons
slots                   Accessing and replacing column slots
