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