RTCGA (version 1.2.2)

getReport: 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]),]
rownames(locations) <- locations[,1]
t1=getDiffExpressedGenes(RTCGASample)
getReport(dataObject=RTCGASample,DGEResult1=t1[[1]],geneLocations=locations)