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
getData                 Extract data from FirehoseData object
getFirehoseAnalyzeDates
                        Get data analyze dates.
getFirehoseData         Get data from Firehose portal.
getFirehoseDatasets     Get a list of TCGA disease 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
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
