Files in PWMEnrich

PWM enrichment analysis

R/AllDataClasses.R R/seqLogoSupp.R R/misc.R R/AllGenerics.R R/diff.R R/PWM-methods.R R/PWMBackground-methods.R R/options.R R/plot.R R/readData.R R/background.R R/pwm.R R/similarity.R R/clover.R R/MotifEnrichmentResults-methods.R R/PWMEnrich-package.R R/MotifEnrichmentReport-methods.R man/PWMCutoffBackground-class.Rd man/groupReport-MotifEnrichmentResults-method.Rd man/MotifEnrichmentResults-class.Rd man/operators-PWMEmpiricalBackground.Rd man/affinitySequenceSet.Rd man/makePWMLognBackground.Rd man/toPWM.Rd man/maxAligned.Rd man/makeStartEndPos.Rd man/gevPerSequence.Rd man/plotMultipleMotifs.Rd man/dot-inputPFMfromMatrixOrPWM.Rd man/motifRankingForGroup-MotifEnrichmentResults-method.Rd man/logNormPval.Rd man/operators-PWMCutoffBackground.Rd man/makePriors.Rd man/show-PWMLognBackground-method.Rd man/readJASPAR.Rd man/divideRows.Rd man/dot-normalize.bg.seq.Rd man/empiricalPvalueSequenceSet.Rd man/motifDiffEnrichment.Rd man/subsetting-PWMEmpiricalBackground.Rd man/concatenateSequences.Rd man/motifScores.Rd man/operators-PWM.Rd man/PWMLognBackground-class.Rd man/cutoffZscore.Rd man/operators-MotifEnrichmentResults.Rd man/subsetting-PWMGEVBackground.Rd man/MotifEnrichmentReport-class.Rd man/operators-PWMLognBackground.Rd man/keepFinite.Rd man/PWM-class.Rd man/subsetting-PWMLognBackground.Rd man/dot-inputParamMotifs.Rd man/matrixShuffleZscorePerSequence.Rd man/PWMUnscaled.Rd man/makePWMEmpiricalBackground.Rd man/motifIC.Rd man/makeBackground.Rd man/PWMGEVBackground-class.Rd man/scanWithPWM.Rd man/operators-MotifEnrichmentReport.Rd man/plotTopMotifsSequence-MotifEnrichmentResults-method.Rd man/motifRankingForSequence-MotifEnrichmentResults-method.Rd man/makePWMPvalCutoffBackgroundFromSeq.Rd man/motifEcdf.Rd man/motifEnrichment.Rd man/makePWMGEVBackground.Rd man/getBackgroundFrequencies.Rd man/sequenceReport-MotifEnrichmentResults-method.Rd man/show-PWMCutoffBackground-method.Rd man/plotTopMotifsGroup-MotifEnrichmentResults-method.Rd man/makePWMPvalCutoffBackground.Rd man/cloverPvalue1seq.Rd man/subsetting-PWMCutoffBackground.Rd man/dot-normargPriorParams.Rd man/readTRANSFAC.Rd man/motifRecoveryAUC.Rd man/PWMEmpiricalBackground-class.Rd man/show-PWMEmpiricalBackground-method.Rd man/makePWMCutoffBackground.Rd man/dot-normargPfm.Rd man/show-PWMGEVBackground-method.Rd man/colMedians.Rd man/PWMEnrich-package.Rd man/motifPrAUC.Rd man/getPromoters.Rd man/empiricalPvalue.Rd man/tryAllMotifAlignments.Rd man/show-PWM-method.Rd man/dot-inputParamSequences.Rd man/useBigMemoryPWMEnrich.Rd man/plot-MotifEnrichmentReport-missing-method.Rd man/rankingProcessAndReturn.Rd man/motifScoresBigMemory.Rd man/seqLogoGrid.Rd man/readMotifs.Rd man/cloverScore.Rd man/colSds.Rd man/plotPFM.Rd man/motifSimilarity.Rd man/reverseComplement-PWM-method.Rd man/plotMotifScores.Rd man/DNAStringSetToList.Rd man/show-MotifEnrichmentReport-method.Rd man/registerCoresPWMEnrich.Rd man/cutoffZscoreSequenceSet.Rd man/PFMtoPWM.Rd man/operators-PWMGEVBackground.Rd man/logNormPvalSequenceSet.Rd man/plot-PWM-missing-method.Rd man/as.data.frame-MotifEnrichmentReport-method.Rd man/show-MotifEnrichmentResults-method.Rd tests/test-all.R inst/doc/PWMEnrich.pdf inst/doc/PWMEnrich.R inst/tests/test_similarity.R inst/tests/test_motifEnrichment.R inst/tests/test_invalidInput.R inst/tests/test_clover.R