MotifEnrichmentReport   A report class with formatted results of motif
                        enrichment
MotifEnrichmentResults
                        A wrapper class for results of
                        motifEnrichment() that should make it easier to
                        access the results.
PFMtoPWM                Convert frequencies into motifs using
                        PWMUnscaled
PWM                     A class that represents a Position Weight
                        Matrix (PWM)
PWMCutoffBackground     Hit count background distribution for a set of
                        PWMs
PWMEmpiricalBackground
                        Background for calculating empirical P-values
PWMGEVBackground        Generalized Extreme Values (GEV) background for
                        P-values
PWMLognBackground       Lognormal background distribution for a set of
                        PWMs
PWMUnscaled             Create a PWM from PFM
[,PWMCutoffBackground-method
                        Get the background for a subset of PWMs
[,PWMEmpiricalBackground-method
                        Get the background for a subset of PWMs
[,PWMGEVBackground-method
                        Get the background for a subset of PWMs
[,PWMLognBackground-method
                        Get the background for a subset of PWMs
as.data.frame,MotifEnrichmentReport-method
                        Convert a MotifEnrichmentReport into a
                        data.frame object
getBackgroundFrequencies
                        Get the four nucleotides background frequencies
groupReport,MotifEnrichmentResults-method
                        Generate a motif enrichment report for the
                        whole group of sequences together
makeBackground          Make a background for a set of position
                        frequency matrices
makePWMCutoffBackground
                        Make a cutoff background
makePWMEmpiricalBackground
                        Make an empirical P-value background
makePWMGEVBackground    Make a GEV background distribution
makePWMLognBackground   Make a lognormal background distribution
makePWMPvalCutoffBackground
                        Construct a cutoff background from empirical
                        background
makePWMPvalCutoffBackgroundFromSeq
                        Construct a P-value cutoff background from a
                        set of sequences
makePriors              Make priors from background sequences
motifDiffEnrichment     Differential motif enrichment
motifEcdf               Calculate the empirical distribution score
                        distribution for a set of motifs
motifEnrichment         Motif enrichment
motifIC                 Information content for a PWM or PFM
motifRankingForGroup,MotifEnrichmentResults-method
                        Get a ranking of motifs by their enrichment in
                        the whole set of sequences
motifRankingForSequence,MotifEnrichmentResults-method
                        Get a ranking of motifs by their enrichment in
                        one specific sequence
motifScores             Motif affinity of number of hits over a
                        threshold
motifSimilarity         Calculates similarity between two PFMs.
names,MotifEnrichmentReport
                        Names of variables
names,MotifEnrichmentResults
                        Names of variables
names,PWM               Names of variables
names,PWMCutoffBackground
                        Names of variables
names,PWMEmpiricalBackground
                        Names of variables
names,PWMGEVBackground
                        Names of variables
names,PWMLognBackground
                        Names of variables
plot                    Plotting for the PWM class
plotMotifScores         Plot the raw motifs scores as returned by
                        motifScores()
plotMultipleMotifs      Plot mulitple motifs in a single plot
plotTopMotifsGroup,MotifEnrichmentResults-method
                        Plot the top N enrichment motifs in a group of
                        sequences
plotTopMotifsSequence,MotifEnrichmentResults-method
                        Plot the top N enrichment motifs in a single
                        sequence
readMotifs              Read in motifs in JASPAR or TRANSFAC format
registerCoresPWMEnrich
                        Register than PWMEnrich can use parallel CPU
                        cores
reverseComplement       Reverse complement for the PWM object
scanWithPWM             Scan the whole sequence on both strands
seqLogoGrid             Draw a motif logo on an existing viewport
sequenceReport,MotifEnrichmentResults-method
                        Generate a motif enrichment report for a single
                        sequence
toPWM                   Convert motifs into PWMs
useBigMemoryPWMEnrich   If to use a faster implementation of motif
                        scanning that requires abount 5 to 10 times
                        more memory
