R: Draws a circle plot into working directory

getReport {RTCGAToolbox}

R Documentation

Draws a circle plot into working directory

Description

getReport draws a circle plot into your workin director to show log fold changes for differentially expressed genes, copy number alterations and mutations.

Usage

getReport(dataObject, DGEResult1 = NULL, DGEResult2 = NULL, geneLocations)

Arguments

`dataObject`	This must be `FirehoseData` object.
`DGEResult1`	Differential gene expression results object (Optional)
`DGEResult2`	Differential gene expression results object (Optional)
`geneLocations`	Gene coordinates.

Value

Draws a circle plot

Examples

data(RTCGASample)
require("Homo.sapiens")
locations <- genes(Homo.sapiens,columns="SYMBOL")
locations <- as.data.frame(locations)
locations <- locations[,c(6,1,5,2:3)]
locations <- locations[!is.na(locations[,1]),]
locations <- locations[!duplicated(locations[,1]),]
rownames(locations) <- locations[,1]
t1 <- getDiffExpressedGenes(RTCGASample)
## Not run: 
getReport(dataObject=RTCGASample,DGEResult1=t1[[1]],geneLocations=locations)

## End(Not run)

[Package RTCGAToolbox version 2.10.0 Index]