CorResult-class         An S4 class to store correlations between gene
                        expression level and copy number data
DGEResult-class         An S4 class to store differential gene
                        expression results
FirehoseCGHArray-class
                        An S4 class to store data from CGA platforms
FirehoseData-class      An S4 class to store main data object from
                        clinent function.
FirehoseGISTIC-class    An S4 class to store processed copy number
                        data. (Data processed by using GISTIC2
                        algorithm)
FirehoseMethylationArray-class
                        An S4 class to store data from methylation
                        platforms
FirehosemRNAArray-class
                        An S4 class to store data from array (mRNA,
                        miRNA etc.) platforms
RTCGAToolbox            RTCGAToolbox: A New Tool for Exporting TCGA
                        Firehose Data
accmini                 A subset of the Adrenocortical Carcinoma (ACC)
                        dataset
biocExtract             Extract and convert data from a 'FirehoseData'
                        object to a 'Bioconductor' object
getBroadSubtypes        Download expression-based cancer subtypes from
                        the Broad Institute
getCNGECorrelation      Perform correlation analysis between gene
                        expression and copy number data
getData                 Extract data from FirehoseData object
getDiffExpressedGenes   Perform differential gene expression analysis
                        for mRNA expression data.
getFirehoseAnalyzeDates
                        Get data analyze dates.
getFirehoseData         Get data from Firehose portal.
getFirehoseDatasets     Get list of TCGA cohorts.
getFirehoseRunningDates
                        Get standard data running dates.
getGISTICPeaks          Download GISTIC2 peak-level data from the
                        Firehose pipeline
getLinks                Get resource links from inputs
getMutationRate         Make a table for mutation rate of each gene in
                        the cohort
getReport               Draws a circle plot into working directory
getSurvival             Perform survival analysis based on gene
                        expression data
hg19.ucsc.gene.locations
                        Gene coordinates for circle plot.
makeSummarizedExperimentFromGISTIC
                        Create a SummarizedExperiment from FireHose
                        GISTIC
selectType              Accessor function for the FirehoseData object
showResults             Export toptable or correlation data frame
showResults,CorResult-method
                        Export toptable or correlation data frame
showResults,DGEResult-method
                        Export toptable or correlation data frame
