absoluteRiskCI | Calculate upper and lower boudaries for the absolute risk... |
adjustRisk | Use with caution! These are based on estimates of what we... |
copyNumberMountainPlot | Windowed, scaled CN values across the genome |
dot-plotSegmentedGenome | Recommend that this not be used directly. segmentRawData... |
loadSampleInformation | Set up the sample information required for analysis. |
patientEndoscopyPlot | Over time per endoscopy risk plot |
patientRiskTilesPlot | Per sample over time tile risk plot |
plotCorrectedCoverage | Plot genome-wide coverage from adjusted raw data |
plotSegmentData | Plot genome-wide raw and segmented values for all samples in... |
predictions | Get predictions from the model |
predictRiskFromSegments | Get the per-sample residuals calculated from the segmentation... |
relativeRiskCI | Calculate upper and lower boudaries for the relative risk... |
riskColors | Get the colors used for risk classes 'low', 'moderate','high' |
runQDNAseq | Run QNDAseq on bam files using previously determined... |
rx | Times per sample are determined by the order of the sample as... |
rxRules | Times per sample are determined by the order of the sample as... |
sampleNames | Get the samplenames |
sampleResiduals | Get the per-sample residuals calculated from the segmentation... |
scoreCX | Per-sample complexity score. |
segmentedValues | Get the segmented values for samples from the segmentation... |
segmentRawData | This function runs the copynumber::pcf algorithm to segment... |
showModelPredictions | Model predictions plot |
showPredictionCalibration | Predictions risk calibration plot |
subtractArms | Subtract arm-level values from smaller tile sizes. Used only... |
tileSegments | Presumes that the segmented data has already been filtered... |
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