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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 |
| .inputParamMotifs | Normalizes the motifs input argument for multiple functions... |
| .inputParamSequences | Normalize the sequences input argument... |
| .inputPFMfromMatrixOrPWM | Check the frequency matrix input parameter for motifSimilarity... |
| .normalize.bg.seq | check consistency of bg... |
| .normargPfm | Input parameter normalization for PWMUnscaled... |
| .normargPriorParams | Input parameter normalization function for PWMUnscaled... |
| 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... |
| DNAStringSetToList | Convert DNAStringSet to list of DNAString objects... |
| 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... |
| length | Names of variables |
| length-method | Names of variables |
| 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... |
| 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... |
| makeStartEndPos | Divide total... |
| matrixShuffleZscorePerSequence | Obtain z-score for motif column shuffling... |
| maxAligned | Returned the aligned motif parts... |
| motifDiffEnrichment | Differential motif enrichment |
| motifEnrichment | 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... |
| motifPrAUC | Calculate PR-AUC for motifs ranked according to some scoring scheme... |
| 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... |
| 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-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... |
| pickGenome | A helper function to pick a genome for an organism... |
| plot | Plotting for the PWM class... |
| plot-method | Plotting for the PWM class... |
| plotMultipleMotifs | Plot mulitple motifs in a single plot... |
| plotPFM | Plot a PFM (not PWM) using seqLogo... |
| 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 |
| 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 | 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... |
| show-method | show method for MotifEnrichmentResults... |
| show-method | show method for PWM... |
| show-method | show method for PWMCutoffBackground... |
| show-method | show method for PWMEmpiricalBackground... |
| show-method | show method for PWMGEVBackground... |
| show-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... |