A Tool to Analyze and Design NGS Based Custom Gene Panels


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Documentation for package ‘PrecisionTrialDrawer’ version 1.0.1

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PrecisionTrialDrawer-package PrecisionTrialDrawer: a package to analyze and design custom cancer panels
appendRepo appendRepo: Add extra population data
appendRepo-method Class 'CancerPanel'
CancerPanel-class Class 'CancerPanel'
coocMutexPlot Plot cooccurence and mutual exclusivity between pairs of drugs or genes
coocMutexPlot-method Class 'CancerPanel'
coveragePlot A series of bar charts representing the number of samples harbouring at least one or more alterations
coveragePlot-method Class 'CancerPanel'
coverageStackPlot A stacked and beside bar chart representing a breakdown of covered samples
coverageStackPlot-method Class 'CancerPanel'
cpArguments Method that returns the 'arguments' slot in a 'CancerPanel' object.
cpArguments-method Class 'CancerPanel'
cpData Method that returns the 'dataFull' slot in a 'CancerPanel' object.
cpData-method Class 'CancerPanel'
cpDataSubset Method that returns the 'dataSubset' slot in a 'CancerPanel' object.
cpDataSubset-method Class 'CancerPanel'
cpDesign Example of a cancer panel design export
cpFreq Calculate frequencies of mutations, copynumber, fusion or expression on a CancerPanel object
cpFreq-method Class 'CancerPanel'
cpObj Example of a cancer panel
cpObj2 Example of a cancer panel
dataExtractor dataExtractor: extract data from a CancerPanel object
dataExtractor-method Class 'CancerPanel'
filterFusions filterFusions: remove or keep specified fusions
filterFusions-method Class 'CancerPanel'
filterMutations filterMutations: remove or keep specified mutations
filterMutations-method Class 'CancerPanel'
getAlterations Retrieve genomic data for each gene in the panel
getAlterations-method Class 'CancerPanel'
newCancerPanel CancerPanel object constructor
panelDesigner Estimate panel design according to user specifications
panelDesigner-method Class 'CancerPanel'
panelexample Example of a cancer panel
panelOptimizer A function that open a shiny app to optimize panel size while retaining the majority of mutations
panelOptimizer-method Class 'CancerPanel'
PrecisionTrialDrawer PrecisionTrialDrawer: a package to analyze and design custom cancer panels
propPowerSampleSize Calculate sample size or power required in a 2-sample or 1-sample proportion equality study
propPowerSampleSize-method Class 'CancerPanel'
saturationPlot Plot your panel along with incremental genomic space occupied adding one piece at a time
saturationPlot-method Class 'CancerPanel'
show-method Class 'CancerPanel'
showCancerStudy List of cancer studies included in the cBioportal
showTumorType List of tumor type barcode
subsetAlterations Retrieve exactly the the alteration requested in the panel after a getAlterations method
subsetAlterations-method Class 'CancerPanel'
survPowerSampleSize Calculate sample size or power required in a 2-sample time-to-event (survival) study
survPowerSampleSize-method Class 'CancerPanel'
survPowerSampleSize1Arm Calculate sample size or power required in a 1-sample time-to-event (survival) study
survPowerSampleSize1Arm-method Class 'CancerPanel'