CancerPanel-class {PrecisionTrialDrawer} | R Documentation

## Class `CancerPanel`

### Description

Class `CancerPanel` defines an object (S4 class) that contains data and custom arguments to run panel simulations and panel designs.

### Value

Class object

### Objects from the Class

Objects can be created by calls of the form `newCancerPanel(panel, padding_length , utr)`.

### Constructor

newCancerPanel(panel=data.frame, padding_length=numeric , utr=logical)

### Slots

`arguments`

  Object of class `list` containing the all panel related information. It is filled during the `CancerPanel` object construction.

`dataFull`

  Object of class `list` containing all the alterations for all the genes in the panel and every tumor type requested. It is filled by the `getAlterations` method.

`dataSubset`

  Object of class `list` containing all the alteration requested. It is filled by the `subsetAlterations` method. Every alteration type is defined by a slot; all slots have the same data.frame layout.

### Methods

show

  `show(object = "CancerPanel")`: ...

getAlterations

  `getAlterations(object = "CancerPanel")`: ...

subsetAlterations

  `subsetAlterations(object = "CancerPanel")`: ...

panelDesigner

  `panelDesigner(object = "CancerPanel")`: ...

cpArguments

  `cpArguments(object = "CancerPanel")`: ...

cpData

  `cpData(object = "CancerPanel")`: ...

cpDataSubset

  `cpDataSubset(object = "CancerPanel")`: ...

coveragePlot

  `coveragePlot(object = "CancerPanel")`: ...

coverageStackPlot

  `coverageStackPlot(object = "CancerPanel")`: ...

saturationPlot

  `saturationPlot(object = "CancerPanel")`: ...

coocMutexPlot

  `coocMutexPlot(object = "CancerPanel")`: ...

survPowerSampleSize

  `survPowerSampleSize(object = "CancerPanel")`: ...

survPowerSampleSize1Arm

  `survPowerSampleSize(object = "CancerPanel")`: ...

cpFreq

  `cpFreq(object = "CancerPanel")`: ...

panelOptimizer

  `panelOptimizer(object = "CancerPanel")`: ...

appendRepo

  `appendRepo(object = "CancerPanel")`: ...

dataExtractor

  `dataExtractor(object = "CancerPanel")`: ...

propPowerSampleSize

  `propPowerSampleSize(object = "CancerPanel")`: ...

filterMutations

  `filterMutations(object = "CancerPanel")`: ...

filterFusions

  `filterFusions(object = "CancerPanel")`: ...

### See Also

`newCancerPanel`

### Examples

    showClass("CancerPanel")

[Package PrecisionTrialDrawer version 1.2.1 Index]