getReport: Draws a circle plot into working directory

In RTCGAToolbox: A new tool for exporting TCGA Firehose data

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(accmini)
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]
## Not run: 
  getReport(dataObject=accmini,DGEResult1=t1[[1]],geneLocations=locations)

## End(Not run)

RTCGAToolbox documentation built on Nov. 8, 2020, 5:34 p.m.