getReport: Make report plot.

In RTCGAToolbox: A new tool for exporting TCGA Firehose data

Description

This function provides a circle plot from "FirehoseData" data object. Current function reports differentially expressed genes, copy number values and mutations. Function can take 2 differentially gene expressin analysis results. Users may provide results from 2 different platform. Output will be saved as apdf file.

Usage

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

Arguments

dataObject	: "FirehoseData" object that includes copy number data and mutation data.
DGEResult1	: Differentially gene expression results. Object type must be "DGEResult". Report plot will use fold change value to highlight up and down regulated genes.
DGEResult2	: Differentially gene expression results. Object type must be "DGEResult". Report plot will use fold change value to highlight up and down regulated genes.
geneLocations	: Gene location data frame. RTCGAToolbox provides location for hg19 known genes from UCSC browser. Plese check "RTCGASample" data.

Value

This function creates a pdf file on the working directory that shows the differentially expressed genes, copy number and mutation information.

Author(s)

Mehmet Kemal Samur

Examples

## Not run: 
data(RTCGASample)
data(hg19.ucsc.gene.locations)
t1=getDiffExpressedGenes(a2)
getReport(dataObject=a2,DGEResult1=t1[[1]],geneLocations=hg19.ucsc.gene.locations)
## End(Not run)

RTCGAToolbox documentation built on May 2, 2019, 5:16 p.m.