Background-class        Background class definition
Overlap-class           Overlap class definition
combinatorialDist       Combinatrial model approximation of the number
                        of motif hits
compoundPoissonDist     Compound Poisson Approximation
generateDNAString       Generate DNAString
generateDNAStringSet    Generate DNAStringSet
getAlpha                Accessor to slot alpha
getBeta                 Accessor to slot beta
getBeta3p               Accessor to slot beta3p
getBeta5p               Accessor to slot beta
getCounts               Accessor to slot counts
getGamma                Accessor to slot gamma
getOrder                Accessor to slot order
getSinglestranded       Accessor to slot singlestranded
getStation              Accessor to slot station
getTrans                Accessor to slot trans
lenSequences            Length of sequences in a given fasta file
motifAndBackgroundValid
                        Check valididity of PFM with background
motifEnrichment         Enrichment of motif hits
motifHitProfile         Motif hit profile across multiple sequences
motifHits               Motif hit observations
motifValid              Check valididity of PFM
motifcounter-package    TFBSs analysis in DNA sequences
motifcounterOptions     Set parameters for the enrichment analysis
normalizeMotif          Normalizes a PFM
numMotifHits            Number of motif hits in a set of DNA sequences
probOverlapHit          Overlapping motif hit probabilities
readBackground          Estimates a background model from a set of DNA
                        sequences
revcompMotif            Reverse complements a PFM
scoreDist               Score distribution
scoreDistBf             Score distribution
scoreDistEmpirical      Empirical score distribution
scoreHistogram          Score histogram
scoreHistogramSingleSeq
                        Score histogram on a single sequence
scoreProfile            Score profile across multiple sequences
scoreSequence           Score observations
scoreStrand             Score strand
scoreThreshold          Score threshold
sigLevel                Retrieve the false positive probability
simulateNumHitsDist     Empirical number of motif hits distribution
