.inputPFMfromMatrixOrPWM
                        Check the frequency matrix input parameter for
                        motifSimilarity
.inputParamMotifs       Normalizes the motifs input argument for
                        multiple functions
.inputParamSequences    Normalize the sequences input argument
.normalize.bg.seq       check consistency of bg.seq input parameter
.normargPfm             Input parameter normalization for PWMUnscaled
.normargPriorParams     Input parameter normalization function for
                        PWMUnscaled
DNAStringSetToList      Convert DNAStringSet to list of DNAString
                        objects
MotifEnrichmentReport-class
                        A report class with formatted results of motif
                        enrichment
MotifEnrichmentResults-class
                        A wrapper class for results of
                        motifEnrichment() that should make it easier to
                        access the results.
PFMtoPWM                Convert frequencies into motifs using
                        PWMUnscaled
PWM-class               A class that represents a Position Weight
                        Matrix (PWM)
PWMCutoffBackground-class
                        Hit count background distribution for a set of
                        PWMs
PWMEmpiricalBackground-class
                        Background for calculating empirical P-values
PWMGEVBackground-class
                        Generalized Extreme Values (GEV) background for
                        P-values
PWMLognBackground-class
                        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
affinitySequenceSet     Calculate total affinity over a set of
                        sequences
as.data.frame,MotifEnrichmentReport-method
                        Convert a MotifEnrichmentReport into a
                        data.frame object
cloverPvalue1seq        Calculate the Clover P-value as described in
                        the Clover paper
cloverScore             Calculate the Clover score using the recursive
                        formula from Frith et al
colMedians              Calculate medians of columns
colSds                  Calculate standard deviations of columns
concatenateSequences    Concatenata DNA sequences into a single
                        character object
cutoffZscore            Z-score calculation for cutoff hits
cutoffZscoreSequenceSet
                        Z-score calculation for cutoff hits for group
                        of sequences
divideRows              Divide each row of a matrix with a vector
empiricalPvalue         Calculate the empirical P-value by affinity of
                        cutoff.
empiricalPvalueSequenceSet
                        Empirical P-value for a set of sequences
getBackgroundFrequencies
                        Get the four nucleotides background frequencies
getPromoters            Get the promoter sequences either for a named
                        organism such as "dm3" or a BSgenome object
gevPerSequence          Apply GEV background normalization per every
                        sequence
groupReport,MotifEnrichmentResults-method
                        Generate a motif enrichment report for the
                        whole group of sequences together
keepFinite              Replace all infinite values by 0
logNormPval             Calculate the P-value from lognormal
                        distribution with background of equal length
logNormPvalSequenceSet
                        Lognormal P-value for a set of sequences
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
makeStartEndPos         Divide total.len into fragments of length len
                        by providing start,end positions
matrixShuffleZscorePerSequence
                        Obtain z-score for motif column shuffling
maxAligned              Returned the aligned motif parts
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
motifPrAUC              Calculate PR-AUC for motifs ranked according to
                        some scoring scheme
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
motifRecoveryAUC        Calculate Recovery-AUC for motifs ranked
                        according to some scoring scheme
motifScores             Motif affinity or number of hits over a
                        threshold
motifScoresBigMemory    This is a memory intensive version of
                        motifScore() which is about 2 times faster
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,MotifEnrichmentReport,missing-method
                        Plot the motif enrichment report
plot,PWM,missing-method
                        Plotting for the PWM class
plotMotifScores         Plot the raw motifs scores as returned by
                        motifScores()
plotMultipleMotifs      Plot mulitple motifs in a single plot
plotPFM                 Plot a PFM (not PWM) using seqLogo
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
rankingProcessAndReturn
                        A helper function for motifRankingForGroup and
                        motifRankingForSequence with the common code
readJASPAR              Read motifs in JASPAR format
readMotifs              Read in motifs in JASPAR or TRANSFAC format
readTRANSFAC            Read in motifs in TRANSFAC format
registerCoresPWMEnrich
                        Register than PWMEnrich can use parallel CPU
                        cores
reverseComplement,PWM-method
                        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
show,MotifEnrichmentReport-method
                        show method for MotifEnrichmentReport
show,MotifEnrichmentResults-method
                        show method for MotifEnrichmentResults
show,PWM-method         show method for PWM
show,PWMCutoffBackground-method
                        show method for PWMCutoffBackground
show,PWMEmpiricalBackground-method
                        show method for PWMEmpiricalBackground
show,PWMGEVBackground-method
                        show method for PWMGEVBackground
show,PWMLognBackground-method
                        show method for PWMLognBackground
toPWM                   Convert motifs into PWMs
tryAllMotifAlignments   Try all motif alignments and return max score
useBigMemoryPWMEnrich   If to use a faster implementation of motif
                        scanning that requires abount 5 to 10 times
                        more memory
