# RNA-binding protein motif analysis

## Documentation for package ‘transite’ version 1.0.2

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

## Help Pages

transite-package | transite
.RBPMotif | An S4 class to represent a RBPMotif
.SpectrumScore | An S4 class to represent a scored spectrum
calculateKmerEnrichment | _k_-mer Enrichment between Foreground and Background Sets
calculateKmerScores | _k_-mer Score Calculation
calculateLocalConsistency | Local Consistency Score
calculateMotifEnrichment | Binding Site Enrichment Value Calculation
calculateTranscriptMC | Motif Enrichment calculation
checkKmers | Check Validity of Set of _k_-mers
computeKmerEnrichment | _k_-mer Enrichment between Foreground and Background Sets
computeMotifScore | Motif Score Algorithm
createKmerMotif | Creates Transite motif object from character vector of _k_-mers
createMatrixMotif | Creates Transite motif object from position weight matrix
drawVolcanoPlot | _k_-mer Enrichment Volcano Plot
empiricalEnrichmentMeanCDF | Significance of Observed Mean
ge | Toy Gene Expression Data Set
generateIUPACByKmers | Generates IUPAC code for a character vector of _k_-mers
generateIUPACByMatrix | Generates IUPAC code for motif matrix
generateKmers | _k_-mer Counts for Sequence Set
generateKmersFromIUPAC | Generates all _k_-mers for IUPAC string
generatePermutedEnrichments | Generate Random Permutations of the Enrichment Data
geometricMean | Geometric Mean
getMotifById | Retrieve motif objects by id
getMotifByRBP | Retrieve motif objects by gene symbol
getMotifs | Retrieve list of all motifs
getPPM | Get Position Probability Matrix (PPM) from motif object
homopolymerCorrection | Correction for Homopolymeric Stretches
initIUPAClookupTable | Initializes the IUPAC lookup table
kmers.enrichment | Example _k_-mer Enrichment Data
lookupKmerScores | _k_-mer Score Lookup Table Access Function
motifHeptamers | An S4 class to represent a RBPMotif
motifHeptamers-method | An S4 class to represent a RBPMotif
motifHexamers | An S4 class to represent a RBPMotif
motifHexamers-method | An S4 class to represent a RBPMotif
motifId | An S4 class to represent a RBPMotif
motifId-method | An S4 class to represent a RBPMotif
motifIUPAC | An S4 class to represent a RBPMotif
motifIUPAC-method | An S4 class to represent a RBPMotif
motifLength | An S4 class to represent a RBPMotif
motifLength-method | An S4 class to represent a RBPMotif
motifMatrix | An S4 class to represent a RBPMotif
motifMatrix-method | An S4 class to represent a RBPMotif
motifRbps | An S4 class to represent a RBPMotif
motifRbps-method | An S4 class to represent a RBPMotif
motifs | Transite Motif Database
motifsMetaInfo | Displays motif meta information.
motifSource | An S4 class to represent a RBPMotif
motifSource-method | An S4 class to represent a RBPMotif
motifSpecies | An S4 class to represent a RBPMotif
motifSpecies-method | An S4 class to represent a RBPMotif
motifType | An S4 class to represent a RBPMotif
motifType-method | An S4 class to represent a RBPMotif
pCombine | P-value aggregation
permTestGeometricMean | Permutation Test Based Significance of Observed Mean
plot-method | An S4 class to represent a RBPMotif
plot-method | An S4 class to represent a scored spectrum
RBPMotif-class | An S4 class to represent a RBPMotif
runKmerSPMA | _k_-mer-based Spectrum Motif Analysis
runKmerTSMA | _k_-mer-based Transcript Set Motif Analysis
runMatrixSPMA | Matrix-based Spectrum Motif Analysis
runMatrixTSMA | Matrix-based Transcript Set Motif Analysis
scoreSequences | Score Sequences with PWM
scoreSpectrum | Calculates spectrum scores and creates spectrum plots
scoreTranscripts | Scores transcripts with position weight matrices
scoreTranscriptsSingleMotif | Scores transadsadscripts with position weight matrices
setMotifs | Set Transite motif database
show-method | An S4 class to represent a RBPMotif
show-method | An S4 class to represent a scored spectrum
spectrumAdjRSquared | An S4 class to represent a scored spectrum
spectrumAdjRSquared-method | An S4 class to represent a scored spectrum
spectrumClassifier | Simple spectrum classifier based on empirical thresholds
spectrumConsistencyScore | An S4 class to represent a scored spectrum
spectrumConsistencyScore-method | An S4 class to represent a scored spectrum
spectrumConsistencyScoreN | An S4 class to represent a scored spectrum
spectrumConsistencyScoreN-method | An S4 class to represent a scored spectrum
spectrumConsistencyScorePValue | An S4 class to represent a scored spectrum
spectrumConsistencyScorePValue-method | An S4 class to represent a scored spectrum
spectrumDegree | An S4 class to represent a scored spectrum
spectrumDegree-method | An S4 class to represent a scored spectrum
spectrumFStatistic | An S4 class to represent a scored spectrum
spectrumFStatistic-method | An S4 class to represent a scored spectrum
spectrumFStatisticPValue | An S4 class to represent a scored spectrum
spectrumFStatisticPValue-method | An S4 class to represent a scored spectrum
spectrumResiduals | An S4 class to represent a scored spectrum
spectrumResiduals-method | An S4 class to represent a scored spectrum
SpectrumScore-class | An S4 class to represent a scored spectrum
spectrumSlope | An S4 class to represent a scored spectrum
spectrumSlope-method | An S4 class to represent a scored spectrum
subdivideData | Subdivides Sequences into _n_ Bins
toy.motif.matrix | Toy Motif Matrix
transite | transite