RNA-binding protein motif analysis


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Documentation for package ‘transite’ version 1.2.1

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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
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