API for Bioconductor-mirror/PWMEnrich
PWM enrichment analysis

Global functions
$,MotifEnrichmentReport-method Man page
$,MotifEnrichmentResults-method Man page
$,PWM-method Man page
$,PWMCutoffBackground-method Man page
$,PWMEmpiricalBackground-method Man page
$,PWMGEVBackground-method Man page
$,PWMLognBackground-method Man page
DNAStringSetToList Source code
MotifEnrichmentReport Man page
MotifEnrichmentReport-class Man page
MotifEnrichmentResults Man page
MotifEnrichmentResults-class Man page
PFMtoPWM Man page Source code
PWM Man page
PWM-class Man page
PWMCutoffBackground Man page
PWMCutoffBackground-class Man page
PWMEmpiricalBackground Man page
PWMEmpiricalBackground-class Man page
PWMGEVBackground Man page
PWMGEVBackground-class Man page
PWMLognBackground Man page
PWMLognBackground-class Man page
PWMUnscaled Man page Source code
[,MotifEnrichmentReport-method Man page
[,PWMCutoffBackground-method Man page
[,PWMEmpiricalBackground-method Man page
[,PWMGEVBackground-method Man page
[,PWMLognBackground-method Man page
addLetter Source code
affinitySequenceSet Source code
as.data.frame Man page
as.data.frame,MotifEnrichmentReport-method Man page
cloverPvalue1seq Source code
cloverScore Source code
colMedians Source code
colSds Source code
concatenateSequences Source code
cutoffZscore Source code
cutoffZscoreSequenceSet Source code
divideRows Source code
empiricalPvalue Source code
empiricalPvalueSequenceSet Source code
getBackgroundFrequencies Man page Source code
getPromoters Source code
gevPerSequence Source code
groupReport Man page
groupReport,MotifEnrichmentResults-method Man page
keepFinite Source code
length Man page
length,PWM-method Man page
letterA Source code
letterC Source code
letterG Source code
letterT Source code
logNormPval Source code
logNormPvalSequenceSet Source code
makeBackground Man page Source code
makePWMCutoffBackground Man page Source code
makePWMEmpiricalBackground Man page Source code
makePWMGEVBackground Man page Source code
makePWMLognBackground Man page Source code
makePWMPvalCutoffBackground Man page Source code
makePWMPvalCutoffBackgroundFromSeq Man page Source code
makePriors Man page Source code
makeStartEndPos Source code
matrixShuffleZscorePerSequence Source code
maxAligned Source code
motifDiffEnrichment Man page Source code
motifEcdf Man page Source code
motifEnrichment Man page Source code
motifIC Man page Source code
motifPrAUC Source code
motifRankingForGroup Man page
motifRankingForGroup,MotifEnrichmentResults-method Man page
motifRankingForSequence Man page
motifRankingForSequence,MotifEnrichmentResults-method Man page
motifRecoveryAUC Source code
motifScores Man page Source code
motifScoresBigMemory Source code
motifSimilarity Man page Source code
names,MotifEnrichmentReport Man page
names,MotifEnrichmentReport-method Man page
names,MotifEnrichmentResults Man page
names,MotifEnrichmentResults-method Man page
names,PWM Man page
names,PWM-method Man page
names,PWMCutoffBackground Man page
names,PWMCutoffBackground-method Man page
names,PWMEmpiricalBackground Man page
names,PWMEmpiricalBackground-method Man page
names,PWMGEVBackground Man page
names,PWMGEVBackground-method Man page
names,PWMLognBackground Man page
names,PWMLognBackground-method Man page
normalize.bg.seq Source code
normargPfm Source code
normargPriorParams Source code
nputPFMfromMatrixOrPWM Source code
nputParamMotifs Source code
nputParamSequences Source code
plot Man page
plot,MotifEnrichmentReport,missing-method Man page
plot,PWM,missing-method Man page
plotMotifScores Man page Source code
plotMultipleMotifs Man page Source code
plotPFM Source code
plotTopMotifsGroup Man page
plotTopMotifsGroup,MotifEnrichmentResults-method Man page
plotTopMotifsSequence Man page
plotTopMotifsSequence,MotifEnrichmentResults-method Man page
pwm2cons Source code
pwm2ic Source code
rankingProcessAndReturn Source code
readJASPAR Source code
readMotifs Man page Source code
readTRANSFAC Source code
registerCoresPWMEnrich Man page Source code
reverseComplement Man page
reverseComplement,PWM-method Man page
scanWithPWM Man page Source code
seqLogoGrid Man page Source code
sequenceReport Man page
sequenceReport,MotifEnrichmentResults-method Man page
toPWM Man page Source code
tryAllMotifAlignments Source code
useBigMemoryPWMEnrich Man page Source code
Bioconductor-mirror/PWMEnrich documentation built on May 31, 2017, 9:43 p.m.