A C D E G K L M N P R S T U misc
| affinitySequenceSet | Calculate total affinity over a set of sequences |
| as.data.frame | Convert a MotifEnrichmentReport into a data.frame object |
| as.data.frame-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 |
| 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 |
| 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 | 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 |
| keepFinite | Replace all infinite values by 0 |
| 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 |
| makePWMPvalCutoffBackgroundFromSeq | Construct a P-value cutoff background from a set of 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 |
| 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. |
| 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 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 |
| 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-method | Plot the motif enrichment report |
| 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 |
| 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-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 |
| 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-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 |
| show-method | show method for MotifEnrichmentReport |
| 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 |
| 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 |
| $-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 |
| .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.seq input parameter |
| .normargPfm | Input parameter normalization for PWMUnscaled |
| .normargPriorParams | Input parameter normalization function for PWMUnscaled |
| [-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 |