# R package for analysing TFBSs in DNA sequences

## Documentation for package ‘motifcounter’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

motifcounter-package | TFBSs analysis in DNA sequences
.Background | Background class definition
.Overlap | Overlap class definition
Background-class | Background class definition
clumpSizeDist | Clump size distribution
combinatorialDist | Combinatrial model approximation of the number of motif hits
compoundPoissonDist | Compound Poisson Approximation
computeClumpStartProb | Computes the Clump start probability based on a Markov model
generateDNAString | Generate DNAString
generateDNAStringSet | Generate DNAStringSet
getAlpha | Accessor to slot alpha
getBeta | Accessor to slot beta
getBeta3p | Accessor to slot beta3p
getBeta5p | Accessor to slot beta
getCounts | Accessor to slot counts
getGamma | Accessor to slot gamma
getOrder | Accessor to slot order
getSinglestranded | Accessor to slot singlestranded
getStation | Accessor to slot station
getTrans | Accessor to slot trans
lenSequences | Length of sequences in a given fasta file
markovModel | Markov model for generating Y_1Y_2_Y3 ...
motifAndBackgroundValid | Check valididity of PFM with background
motifcounter | TFBSs analysis in DNA sequences
motifcounterOptions | Set parameters for the enrichment analysis
motifEnrichment | Enrichment of motif hits
motifHitProfile | Motif hit profile across multiple sequences
motifHits | Motif hit observations
motifValid | Check valididity of PFM
normalizeMotif | Normalizes a PFM
numMotifHits | Number of motif hits in a set of DNA sequences
Overlap-class | Overlap class definition
probOverlapHit | Overlapping motif hit probabilities
readBackground | Estimates a background model from a set of DNA sequences
revcompMotif | Reverse complements a PFM
scoreDist | Score distribution
scoreDistBf | Score distribution
scoreDistEmpirical | Empirical score distribution
scoreHistogram | Score histogram
scoreHistogramSingleSeq | Score histogram on a single sequence
scoreProfile | Score profile across multiple sequences
scoreSequence | Score observations
scoreStrand | Score strand
scoreThreshold | Score threshold
sigLevel | Retrieve the false positive probability
simulateClumpSizeDist | Empirical clump size distribution
simulateNumHitsDist | Empirical number of motif hits distribution