AnnotationByFeature-class
                        An S4 class that information on overlap of
                        target features with annotation features
AnnotationByGeneParts-class
                        An S4 class that information on overlap of
                        target features with annotation features
Ops,ScoreMatrix,ScoreMatrix-method
                        Ops method for a ScoreMatrix object. It enables
                        to use arithmetic, indicator and logic
                        operations on ScoreMatrix objects.
Ops,ScoreMatrixList,ScoreMatrixList-method
                        Ops method for a ScoreMatrixList object. It
                        enables to use arithmetic, indicator and logic
                        operations on ScoreMatrixList objects.
Ops,ScoreMatrixList,numeric-method
                        Ops method for a ScoreMatrixList object. It
                        enables to use arithmetic, indicator and logic
                        operations on ScoreMatrixList objects.
Ops,numeric,ScoreMatrixList-method
                        Ops method for a ScoreMatrixList object. It
                        enables to use arithmetic, indicator and logic
                        operations on ScoreMatrixList objects.
RandomEnrichment-class
                        An S4 class for storing 'getRandomEnrichment'
                        function results
ScoreMatrix             Get base-pair score for bases in each window
ScoreMatrix-class       An S4 class for storing 'ScoreMatrix' function
                        results
ScoreMatrixBin          Get bin score for bins on each window
ScoreMatrixList         Make ScoreMatrixList from multiple targets
ScoreMatrixList-class   An S4 class for storing a set of
                        'ScoreMatrixList'
[,ScoreMatrix,ANY,ANY,ANY-method
                        Extract method for a ScoreMatrix object.
[,ScoreMatrixList,ANY,ANY,ANY-method
                        Extract method for a ScoreMatrixList object.
annotateWithFeature     Function to annotate given GRanges object with
                        a given genomic feature
annotateWithFeatureFlank
                        Function to annotate a given GRanges object
                        with promoter,exon,intron & intergenic values
annotateWithFeatures    Annotate given ranges with genomic features
annotateWithGeneParts   Annotate given object with promoter, exon,
                        intron and intergenic regions
binMatrix               Bins the columns of a matrix using a user
                        provided function
c.ScoreMatrix           c.ScoreMatrix
c.ScoreMatrixList       c.ScoreMatrixList
cage                    Example CAGE data set.
calculateOverlapSignificance
                        function that calculates the significance of
                        overlaps of two sets of features using
                        randomization
convertBed2Exons        convert a data frame read-in from a bed file to
                        a GRanges object for exons
convertBed2Introns      convert a data frame read-in from a bed file to
                        a GRanges object for introns
convertBedDf            convert a data frame read-in from a bed file to
                        a GRanges object
cpgi                    Example CpG island data set.
enrichmentMatrix        Compute an enrichment of IP over control both
                        stored in ScoreMatrix objects
enrichmentMatrix,ScoreMatrixList,ScoreMatrix-method
                        Compute an enrichment of IP (stored in
                        ScoreMatrixList object) over control (stored in
                        ScoreMatrix object)
enrichmentMatrix,ScoreMatrixList,ScoreMatrixList-method
                        Compute an enrichment of IP over control both
                        stored in ScoreMatrixList objects
findFeatureComb         Find combitations of genomic features
genes                   Example RefSeq genes data set.
getAssociationWithTSS   Get distance to nearest TSS and gene id from
                        AnnotationByGeneParts
getFeatsWithTargetsStats
                        Get the percentage/count of annotation features
                        overlapping with target features from
                        AnnotationByFeature
getFlanks               Function to get upstream and downstream
                        adjecent regions to a genomic feature such as
                        CpG islands
getMembers              Get the membership slot of AnnotationByFeature
getRandomEnrichment     get enrichment based on randomized feature
                        overlap
getTargetAnnotationStats
                        Get the percentage of target features
                        overlapping with annotation from
                        AnnotationByFeature
gffToGRanges            Converts a gff formated data.frame into a
                        GenomicRanges object.  The GenomicRanges object
                        needs to be properly formated for the function
                        to work.
heatMatrix              Draw a heatmap of a given ScoreMatrix object
heatMeta                Heatmap for meta-region profiles
heatTargetAnnotation    Plots the percentage of overlapping intervals
                        with genomic features in a heatmap
intersectScoreMatrixList
                        Get common rows from all matrices in a
                        ScoreMatrixList object
multiHeatMatrix         Draw multiple heatmaps from a ScoreMatrixList
                        object
orderBy                 Reorder all elements of a ScoreMatrixList to a
                        given ordering vector
patternMatrix           Get scores that correspond to k-mer or PWM
                        matrix occurrence for bases in each window
plotMeta                Line plot(s) for meta-region profiles
plotTargetAnnotation    Plot annotation categories from
                        AnnotationByGeneParts or AnnotationByFeature
promoters               Example promoter data set.
randomizeFeature        function that randomizes the genomic
                        coordinates
readBed                 Read a BED file and convert it to GRanges.
readBroadPeak           A function to read the Encode formatted broad
                        peak file into a GRanges object
readFeatureFlank        A function to read-in genomic features and
                        their upstream and downstream adjecent regions
                        such as CpG islands and their shores
readGeneric             Read a tabular file and convert it to GRanges.
readNarrowPeak          A function to read the Encode formatted
                        narrowPeak file into a GRanges object
readTranscriptFeatures
                        Function for reading exon intron and promoter
                        structure from a given bed file
scaleScoreMatrix        Scales the values in the matrix by rows and/or
                        columns
scaleScoreMatrixList    Scale the ScoreMatrixList
show,RandomEnrichment-method
                        show method for some of the genomation classes
