Man pages for gerstung-lab/BarrettsProgressionRisk
Prognositc adenocarcinoma risk prediction for Barrett's Esophagus

absoluteRiskCICalculate upper and lower boudaries for the absolute risk...
adjustRiskUse with caution! These are based on estimates of what we...
copyNumberMountainPlotWindowed, scaled CN values across the genome
dot-plotSegmentedGenomeRecommend that this not be used directly. segmentRawData...
loadSampleInformationSet up the sample information required for analysis.
patientEndoscopyPlotOver time per endoscopy risk plot
patientRiskTilesPlotPer sample over time tile risk plot
plotCorrectedCoveragePlot genome-wide coverage from adjusted raw data
plotSegmentDataPlot genome-wide raw and segmented values for all samples in...
predictionsGet predictions from the model
predictRiskFromSegmentsGet the per-sample residuals calculated from the segmentation...
relativeRiskCICalculate upper and lower boudaries for the relative risk...
riskColorsGet the colors used for risk classes 'low', 'moderate','high'
runQDNAseqRun QNDAseq on bam files using previously determined...
rxTimes per sample are determined by the order of the sample as...
rxRulesTimes per sample are determined by the order of the sample as...
sampleNamesGet the samplenames
sampleResidualsGet the per-sample residuals calculated from the segmentation...
scoreCXPer-sample complexity score.
segmentedValuesGet the segmented values for samples from the segmentation...
segmentRawDataThis function runs the copynumber::pcf algorithm to segment...
showModelPredictionsModel predictions plot
showPredictionCalibrationPredictions risk calibration plot
subtractArmsSubtract arm-level values from smaller tile sizes. Used only...
tileSegmentsPresumes that the segmented data has already been filtered...
gerstung-lab/BarrettsProgressionRisk documentation built on June 22, 2021, 3:12 p.m.