CancerPanel-class: Class 'CancerPanel'

In gmelloni/PrecisionTrialDesigner: A Tool to Analyze and Design NGS Based Custom Gene Panels

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")

gmelloni/PrecisionTrialDesigner documentation built on March 3, 2023, 6:10 a.m.