# An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification

## Documentation for package ‘transcriptR’ version 1.39.4

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

## Help Pages

addFeature | addFeature
addFeature-method | addFeature
annot | Reference annotation (knownGene from UCSC)
annotateTranscripts | annotateTranscripts
annotateTranscripts-method | annotateTranscripts
breakTranscriptsByPeaks | breakTranscriptsByPeaks
breakTranscriptsByPeaks-method | breakTranscriptsByPeaks
cds | Example of 'ChipDataSet' object.
ChipDataSet | ChipDataSet
ChipDataSet-class | ChipDataSet
constructCDS | constructCDS
constructTDS | constructTDS
detectTranscripts | detectTranscripts
detectTranscripts-method | detectTranscripts
estimateBackground | estimateBackground
estimateBackground-method | estimateBackground
estimateGapDistance | estimateGapDistance
estimateGapDistance-method | estimateGapDistance
exportCoverage | exportCoverage
exportCoverage-method | exportCoverage
getConfusionMatrix | getConfusionMatrix
getConfusionMatrix-method | getConfusionMatrix
getGenomicAnnot | getGenomicAnnot
getGenomicAnnot-method | getGenomicAnnot
getPeaks | getPeaks
getPeaks-method | getPeaks
getPredictorSignificance | getPredictorSignificance
getPredictorSignificance-method | getPredictorSignificance
getProbTreshold | getProbTreshold
getProbTreshold-method | getProbTreshold
getQuadProb | getQuadProb
getQuadProb-method | getQuadProb
getTestedGapDistances | getTestedGapDistances
getTestedGapDistances-method | getTestedGapDistances
getTranscripts | getTranscripts
getTranscripts-method | getTranscripts
peaksToBed | peaksToBed
peaksToBed-method | peaksToBed
plotErrorRate | plotErrorRate
plotErrorRate-method | plotErrorRate
plotFeatures | plotFeatures
plotFeatures-method | plotFeatures
plotGenomicAnnot | plotGenomicAnnot
plotGenomicAnnot-method | plotGenomicAnnot
plotROC | plotROC
plotROC-method | plotROC
predictStrand | predictStrand
predictStrand-method | predictStrand
predictTssOverlap | predictTssOverlap
predictTssOverlap-method | predictTssOverlap
show | Show method for ChipDataSet and TranscriptionDataSet objects
show-method | Show method for ChipDataSet and TranscriptionDataSet objects
tds | Example of 'TranscriptionDataSet' object.
TranscriptionDataSet | TranscriptionDataSet
TranscriptionDataSet-class | TranscriptionDataSet
transcriptsToBed | transcriptsToBed
transcriptsToBed-method | transcriptsToBed