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 2.12.1 Index]