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| 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 |