# A Tool to Analyze and Design NGS Based Custom Gene Panels

## Documentation for package ‘PrecisionTrialDrawer’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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'