API for QDNAseq
Quantitative DNA Sequencing for Chromosomal Aberrations
| Global functions | |
|---|---|
| .binReadCountsPerChunk | Source code |
| .binReadCountsPerSample | Source code |
| LGG150 | Man page |
| QDNAseq | Man page |
| QDNAseq-package | Man page |
| QDNAseqCopyNumbers | Man page |
| QDNAseqCopyNumbers-class | Man page |
| QDNAseqReadCounts | Man page |
| QDNAseqReadCounts-class | Man page |
| QDNAseqSignals | Man page |
| QDNAseqSignals-class | Man page |
| addPhenodata | Man page Source code |
| applyFilters | Man page |
| applyFilters,QDNAseqReadCounts-method | Man page |
| betterCall | Source code |
| binReadCounts | Man page Source code |
| bpend,QDNAseqSignals-method | Man page |
| bpstart,QDNAseqSignals-method | Man page |
| calculateBlacklist | Man page Source code |
| calculateBlacklistByRegions | Man page Source code |
| calculateMappability | Man page Source code |
| callBins | Man page |
| callBins,QDNAseqCopyNumbers-method | Man page |
| chromosomes,QDNAseqSignals-method | Man page |
| compareToReference | Man page |
| compareToReference,QDNAseqCopyNumbers,numeric-method | Man page |
| correctBins | Man page |
| correctBins,QDNAseqReadCounts-method | Man page |
| createBins | Man page Source code |
| downloadBinAnnotations | Man page |
| estimateCorrection | Man page |
| estimateCorrection,QDNAseqReadCounts-method | Man page |
| expectedVariance | Source code |
| exportBins | Man page Source code |
| exportBins,QDNAseqSignals-method | Man page |
| exportSEG | Source code |
| exportVCF | Source code |
| frequencyPlot | Man page |
| frequencyPlot,QDNAseqCopyNumbers,missing-method | Man page |
| getBinAnnotations | Man page Source code |
| highlightFilters | Man page |
| highlightFilters,QDNAseqSignals-method | Man page |
| importReadCounts | Source code |
| isobarPlot | Man page |
| isobarPlot,QDNAseqReadCounts,missing-method | Man page |
| iterateResiduals | Man page Source code |
| log2adhoc | Source code |
| log2offset | Source code |
| makeCgh | Man page |
| makeCgh,QDNAseqCopyNumbers-method | Man page |
| noisePlot | Man page |
| noisePlot,QDNAseqReadCounts,missing-method | Man page |
| normalizeBins | Man page |
| normalizeBins,QDNAseqCopyNumbers-method | Man page |
| normalizeSegmentedBins | Man page |
| normalizeSegmentedBins,QDNAseqCopyNumbers-method | Man page |
| plot | Man page |
| plot,QDNAseqSignals,missing-method | Man page |
| poolRuns | Man page |
| poolRuns,QDNAseqSignals,character-method | Man page |
| sdDiffTrim | Source code |
| segmentBins | Man page |
| segmentBins,QDNAseqCopyNumbers-method | Man page |
| smoothOutlierBins | Man page |
| smoothOutlierBins,QDNAseqCopyNumbers-method | Man page |
| sqrtadhoc | Source code |
| sqrtfactor | Source code |
| sqrtoffset | Source code |
| suppressVerbose | Source code |
| vmsg | Source code |
