$-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 |