Man pages for gmelloni/PrecisionTrialDesigner
A Tool to Analyze and Design NGS Based Custom Gene Panels
| appendRepo | appendRepo: Add extra population data |
| CancerPanel-class | Class 'CancerPanel' |
| coocMutexPlot | Plot cooccurence and mutual exclusivity between pairs of... |
| coveragePlot | A series of bar charts representing the number of samples... |
| coverageStackPlot | A stacked and beside bar chart representing a breakdown of... |
| cpArguments | Method that returns the 'arguments' slot in a 'CancerPanel'... |
| cpData | Method that returns the 'dataFull' slot in a 'CancerPanel'... |
| cpDataSubset | Method that returns the 'dataSubset' slot in a 'CancerPanel'... |
| cpDesign | Example of a cancer panel design export |
| cpFreq | Calculate frequencies of mutations, copynumber, fusion or... |
| cpObj | Example of a cancer panel |
| cpObj2 | Example of a cancer panel |
| dataExtractor | dataExtractor: extract data from a CancerPanel object |
| filterFusions | filterFusions: remove or keep specified fusions |
| filterMutations | filterMutations: remove or keep specified mutations |
| getAlterations | Retrieve genomic data for each gene in the panel |
| newCancerPanel | CancerPanel object constructor |
| panelDesigner | Estimate panel design according to user specifications |
| panelexample | Example of a cancer panel |
| panelOptimizer | A function that open a shiny app to optimize panel size while... |
| PrecisionTrialDrawer-package | PrecisionTrialDrawer: a package to analyze and design custom... |
| propPowerSampleSize | Calculate sample size or power required in a 2-sample or... |
| saturationPlot | Plot your panel along with incremental genomic space occupied... |
| 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... |
| survPowerSampleSize | Calculate sample size or power required in a 2-sample... |
| survPowerSampleSize1Arm | Calculate sample size or power required in a 1-sample... |
