Man pages for motifcounter
R package for analysing TFBSs in DNA sequences

Background-classBackground class definition
clumpSizeDistClump size distribution
combinatorialDistCombinatrial model approximation of the number of motif hits
compoundPoissonDistCompound Poisson Approximation
computeClumpStartProbComputes the Clump start probability based on a Markov model
generateDNAStringGenerate DNAString
generateDNAStringSetGenerate DNAStringSet
getAlphaAccessor to slot alpha
getBetaAccessor to slot beta
getBeta3pAccessor to slot beta3p
getBeta5pAccessor to slot beta
getCountsAccessor to slot counts
getGammaAccessor to slot gamma
getOrderAccessor to slot order
getSinglestrandedAccessor to slot singlestranded
getStationAccessor to slot station
getTransAccessor to slot trans
hitStrandHit strand
lenSequencesLength of sequences in a given fasta file
markovModelMarkov model for generating Y_1Y_2_Y3 ...
motifAndBackgroundValidCheck valididity of PFM with background
motifcounterOptionsSet parameters for the enrichment analysis
motifcounter-packageTFBSs analysis in DNA sequences
motifEnrichmentEnrichment of motif hits
motifHitProfileMotif hit profile across multiple sequences
motifHitsMotif hit observations
motifValidCheck valididity of PFM
normalizeMotifNormalizes a PFM
numMotifHitsNumber of motif hits in a set of DNA sequences
Overlap-classOverlap class definition
probOverlapHitOverlapping motif hit probabilities
readBackgroundEstimates a background model from a set of DNA sequences
revcompMotifReverse complements a PFM
scoreDistScore distribution
scoreDistBfScore distribution
scoreDistEmpiricalEmpirical score distribution
scoreHistogramScore histogram
scoreHistogramSingleSeqScore histogram on a single sequence
scoreProfileScore profile across multiple sequences
scoreSequenceScore observations
scoreStrandScore strand
scoreThresholdScore threshold
sigLevelRetrieve the false positive probability
simulateClumpSizeDistEmpirical clump size distribution
simulateNumHitsDistEmpirical number of motif hits distribution
motifcounter documentation built on Nov. 1, 2018, 4:21 a.m.