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| $-method | Names of variables |
| $-method | Names of variables |
| $-method | Names of variables |
| $-method | Names of variables |
| $-method | Names of variables |
| $-method | Names of variables |
| $-method | Names of variables |
| as.data.frame | Convert a MotifEnrichmentReport into a data.frame object |
| as.data.frame-method | Convert a MotifEnrichmentReport into a data.frame object |
| getBackgroundFrequencies | Get the four nucleotides background frequencies |
| groupReport | Generate a motif enrichment report for the whole group of sequences together |
| groupReport-method | Generate a motif enrichment report for the whole group of sequences together |
| length | Names of variables |
| length-method | Names of variables |
| makeBackground | Make a background for a set of position frequency matrices |
| makePriors | Make priors from background sequences |
| 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 |
| motifDiffEnrichment | Differential motif enrichment |
| motifEcdf | Calculate the empirical distribution score distribution for a set of motifs |
| motifEnrichment | Motif enrichment |
| MotifEnrichmentReport | A report class with formatted results of motif enrichment |
| MotifEnrichmentReport-class | 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. |
| MotifEnrichmentResults-class | A wrapper class for results of motifEnrichment() that should make it easier to access the results. |
| motifIC | Information content for a PWM or PFM |
| motifRankingForGroup | Get a ranking of motifs by their enrichment in the whole set of sequences |
| motifRankingForGroup-method | Get a ranking of motifs by their enrichment in the whole set of sequences |
| motifRankingForSequence | Get a ranking of motifs by their enrichment in one specific sequence |
| motifRankingForSequence-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 |
| names-method | Names of variables |
| names-method | Names of variables |
| names-method | Names of variables |
| names-method | Names of variables |
| names-method | Names of variables |
| names-method | Names of variables |
| names-method | Names of variables |
| PFMtoPWM | Convert frequencies into motifs using PWMUnscaled |
| plot | Plotting for the PWM class |
| plot-method | Plotting for the PWM class |
| plotMotifScores | Plot the raw motifs scores as returned by motifScores() |
| plotMultipleMotifs | Plot mulitple motifs in a single plot |
| plotTopMotifsGroup | Plot the top N enrichment motifs in a group of sequences |
| plotTopMotifsGroup-method | Plot the top N enrichment motifs in a group of sequences |
| plotTopMotifsSequence | Plot the top N enrichment motifs in a single sequence |
| plotTopMotifsSequence-method | Plot the top N enrichment motifs in a single sequence |
| PWM | A class that represents a Position Weight Matrix (PWM) |
| PWM-class | A class that represents a Position Weight Matrix (PWM) |
| PWMCutoffBackground | Hit count background distribution for a set of PWMs |
| PWMCutoffBackground-class | Hit count background distribution for a set of PWMs |
| PWMEmpiricalBackground | Background for calculating empirical P-values |
| PWMEmpiricalBackground-class | Background for calculating empirical P-values |
| PWMGEVBackground | Generalized Extreme Values (GEV) background for P-values |
| PWMGEVBackground-class | Generalized Extreme Values (GEV) background for P-values |
| PWMLognBackground | Lognormal background distribution for a set of PWMs |
| PWMLognBackground-class | Lognormal background distribution for a set of PWMs |
| PWMUnscaled | Create a PWM from PFM |
| 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 |
| reverseComplement-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 | Generate a motif enrichment report for a single sequence |
| sequenceReport-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 |
| [-method | Names of variables |
| [-method | Get the background for a subset of PWMs |
| [-method | Get the background for a subset of PWMs |
| [-method | Get the background for a subset of PWMs |
| [-method | Get the background for a subset of PWMs |