![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| 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' |