Man pages for PWMEnrich
PWM enrichment analysis a MotifEnrichmentReport into a data.frame object
getBackgroundFrequenciesGet the four nucleotides background frequencies
groupReport-commaMotifEnrichmentResults-methodGenerate a motif enrichment report for the whole group of...
makeBackgroundMake a background for a set of position frequency matrices
makePriorsMake priors from background sequences
makePWMCutoffBackgroundMake a cutoff background
makePWMEmpiricalBackgroundMake an empirical P-value background
makePWMGEVBackgroundMake a GEV background distribution
makePWMLognBackgroundMake a lognormal background distribution
makePWMPvalCutoffBackgroundConstruct a cutoff background from empirical background
makePWMPvalCutoffBackgroundFromSeqConstruct a P-value cutoff background from a set of sequences
motifDiffEnrichmentDifferential motif enrichment
motifEcdfCalculate the empirical distribution score distribution for a...
motifEnrichmentMotif enrichment
MotifEnrichmentReportA report class with formatted results of motif enrichment
MotifEnrichmentResultsA wrapper class for results of motifEnrichment() that should...
motifICInformation content for a PWM or PFM
motifRankingForGroup-commaMotifEnrichmentResults-methodGet a ranking of motifs by their enrichment in the whole set...
motifRankingForSequence-commaMotifEnrichmentResults-methodGet a ranking of motifs by their enrichment in one specific...
motifScoresMotif affinity of number of hits over a threshold
motifSimilarityCalculates similarity between two PFMs.
operators-MotifEnrichmentReportNames of variables
operators-MotifEnrichmentResultsNames of variables
operators-PWMNames of variables
operators-PWMCutoffBackgroundNames of variables
operators-PWMEmpiricalBackgroundNames of variables
operators-PWMGEVBackgroundNames of variables
operators-PWMLognBackgroundNames of variables
PFMtoPWMConvert frequencies into motifs using PWMUnscaled
plotPlotting for the PWM class
plotMotifScoresPlot the raw motifs scores as returned by motifScores()
plotMultipleMotifsPlot mulitple motifs in a single plot
plotTopMotifsGroup-commaMotifEnrichmentResults-methodPlot the top N enrichment motifs in a group of sequences
plotTopMotifsSequence-commaMotifEnrichmentResults-methodPlot the top N enrichment motifs in a single sequence
PWMA class that represents a Position Weight Matrix (PWM)
PWMCutoffBackgroundHit count background distribution for a set of PWMs
PWMEmpiricalBackgroundBackground for calculating empirical P-values
PWMGEVBackgroundGeneralized Extreme Values (GEV) background for P-values
PWMLognBackgroundLognormal background distribution for a set of PWMs
PWMUnscaledCreate a PWM from PFM
readMotifsRead in motifs in JASPAR or TRANSFAC format
registerCoresPWMEnrichRegister than PWMEnrich can use parallel CPU cores
reverseComplementReverse complement for the PWM object
scanWithPWMScan the whole sequence on both strands
seqLogoGridDraw a motif logo on an existing viewport
sequenceReport-commaMotifEnrichmentResults-methodGenerate a motif enrichment report for a single sequence
subsetting-PWMCutoffBackgroundGet the background for a subset of PWMs
subsetting-PWMEmpiricalBackgroundGet the background for a subset of PWMs
subsetting-PWMGEVBackgroundGet the background for a subset of PWMs
subsetting-PWMLognBackgroundGet the background for a subset of PWMs
toPWMConvert motifs into PWMs
useBigMemoryPWMEnrichIf to use a faster implementation of motif scanning that...
PWMEnrich documentation built on Nov. 1, 2018, 2:25 a.m.