Man pages for PWMEnrich
PWM enrichment analysis
| affinitySequenceSet | Calculate total affinity over a set of sequences |
| as.data.frame-MotifEnrichmentReport-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... |
| 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 |
| dot-inputParamMotifs | Normalizes the motifs input argument for multiple functions |
| dot-inputParamSequences | Normalize the sequences input argument |
| dot-inputPFMfromMatrixOrPWM | Check the frequency matrix input parameter for... |
| dot-normalize.bg.seq | check consistency of bg.seq input parameter |
| dot-normargPfm | Input parameter normalization for PWMUnscaled |
| dot-normargPriorParams | Input parameter normalization function for PWMUnscaled |
| 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... |
| gevPerSequence | Apply GEV background normalization per every sequence |
| groupReport-MotifEnrichmentResults-method | Generate a motif enrichment report for the whole group of... |
| keepFinite | Replace all infinite values by 0 |
| logNormPval | Calculate the P-value from lognormal distribution with... |
| 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... |
| 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... |
| 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... |
| motifIC | Information content for a PWM or PFM |
| motifPrAUC | Calculate PR-AUC for motifs ranked according to some scoring... |
| motifRankingForGroup-MotifEnrichmentResults-method | Get a ranking of motifs by their enrichment in the whole set... |
| motifRankingForSequence-MotifEnrichmentResults-method | Get a ranking of motifs by their enrichment in one specific... |
| motifRecoveryAUC | Calculate Recovery-AUC for motifs ranked according to some... |
| motifScores | Motif affinity or number of hits over a threshold |
| motifScoresBigMemory | This is a memory intensive version of motifScore() which is... |
| motifSimilarity | Calculates similarity between two PFMs. |
| operators-MotifEnrichmentReport | Names of variables |
| operators-MotifEnrichmentResults | Names of variables |
| operators-PWM | Names of variables |
| operators-PWMCutoffBackground | Names of variables |
| operators-PWMEmpiricalBackground | Names of variables |
| operators-PWMGEVBackground | Names of variables |
| operators-PWMLognBackground | Names of variables |
| PFMtoPWM | Convert frequencies into motifs using PWMUnscaled |
| plot-MotifEnrichmentReport-missing-method | Plot the motif enrichment report |
| 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 |
| plot-PWM-missing-method | Plotting for the PWM class |
| 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 |
| 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 |
| PWMEnrich-package | PWMEnrich: PWM enrichment analysis |
| 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... |
| 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 |
| sequenceReport-MotifEnrichmentResults-method | Generate a motif enrichment report for a single sequence |
| show-MotifEnrichmentReport-method | show method for MotifEnrichmentReport |
| show-MotifEnrichmentResults-method | show method for MotifEnrichmentResults |
| 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 |
| show-PWM-method | show method for PWM |
| subsetting-PWMCutoffBackground | Get the background for a subset of PWMs |
| subsetting-PWMEmpiricalBackground | Get the background for a subset of PWMs |
| subsetting-PWMGEVBackground | Get the background for a subset of PWMs |
| subsetting-PWMLognBackground | Get the background for a subset of PWMs |
| 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... |
