convertSEMsToPPMs       Convert a SNP Effect Matrix to a position
                        probability matrices (PPMs)
enrichmentSets          Run the Full Differential‐Expression Motif
                        Enrichment Pipeline
enrichSEMs              Calculates binding enrichment for motif(s)
getBaseline             Access baseline from a SNPEffectMatrix object
getRanges               Access ranges slot in a SEMScores object
getRangeSeqs            Get sequence for genomic ranges and variants
getSEM                  Access the SEM from a SNPEffectMatrix object
getSEMId                Access semId from a SNPEffectMatrix object
getSEMs                 Access sems matrix from a
                        SNPEffectMatrixCollection object
loadSEMCollection       Load .sem files and meta data into a
                        SNPEffectMatrixCollection
plotEnrich              Plot the results of 'enrichSEMs'
plotSEM                 Plot SEM scores for each nucleic acid in each
                        position of the motif
plotSEMMotifs           Plot non-alt versus alt binding propensity for
                        a single variant
plotSEMVariants         Plot non-alt versus alt binding propensity for
                        a single motif
scoreBinding            Calculate binding propensity for all SEM motifs
                        and genomic positions provided
scoreVariants           Calculate risk/non-risk binding propensity for
                        all SEM motifs and variants provided
SEMC                    Default SNP Effect Matrix Data Collection
semData                 Accessor semData slot in a SEMScores object
SEMScores               SEMScores object and constructor
SEMScores-class         Class for storing SEM motif binding
                        calculations for multiple genomic ranges or
                        variants
show,SEMScores-method   Show method for SEMScores objects
show,SNPEffectMatrix-method
                        Show for SNPEffectMatrix
show,SNPEffectMatrixCollection-method
                        Show method for SNPEffectMatrixCollection
                        objects
SNPEffectMatrix         SNPEffectMatrix object and constructor
SNPEffectMatrix-class   SNP Effect Matrix (SEM)
SNPEffectMatrixCollection
                        SNPEffectMatrixCollection object and
                        constructor
SNPEffectMatrixCollection-class
                        A collection of SNPEffectMatrix objects and
                        their corresponding meta data
