.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...
.normargPfm             Input parameter normalization for
                        PWMUnscaled...
.normargPriorParams     Input parameter normalization function for
                        PWMUnscaled...
DNAStringSetToList      Convert DNAStringSet to list of DNAString
                        objects...
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
affinitySequenceSet     Calculate total affinity over a set of
                        sequences...
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...
gevPerSequence          Apply GEV background normalization per every
                        sequence...
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...
makePriors              Make priors from background sequences...
makeStartEndPos         Divide total...
matrixShuffleZscorePerSequence
                        Obtain z-score for motif column shuffling...
maxAligned              Returned the aligned motif parts...
motifDiffEnrichment     Differential motif enrichment
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 of number of hits over a
                        threshold...
motifScoresBigMemory    This is a memory intensive version of
                        motifScore() which is abount 2 times faster...
motifSimilarity         Calculates similarity between two PFMs.
names,MotifEnrichmentResults-method
                        Names of variables
names,PWM-method        Names of variables
names,PWMCutoffBackground-method
                        Names of variables
names,PWMEmpiricalBackground-method
                        Names of variables
names,PWMGEVBackground-method
                        Names of variables
names,PWMLognBackground-method
                        Names of variables
pickGenome              A helper function to pick a genome for an
                        organism...
plot,PWM,missing-method
                        Plotting for the PWM class...
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...
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...
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...
