# A new tool for exporting TCGA Firehose data

## Documentation for package ‘RTCGAToolbox’ version 2.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

accmini | A subset of the Adrenocortical Carcinoma (ACC) dataset
biocExtract | Extract and convert data from a 'FirehoseData' object to a 'Bioconductor' object
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
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
getData-method | An S4 class to store main data object from clinent function.
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.
isEmpty-method | An S4 class to store processed copy number data. (Data processed by using GISTIC2 algorithm)
makeSummarizedExperimentFromGISTIC | Create a SummarizedExperiment from FireHose GISTIC
RTCGAToolbox | RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
selectType | Accessor function for the FirehoseData object
selectType-method | An S4 class to store main data object from clinent function.
show-method | An S4 class to store main data object from clinent function.
showResults | Export toptable or correlation data frame
showResults-method | Export toptable or correlation data frame
showResults-method | Export toptable or correlation data frame
updateObject-method | An S4 class to store main data object from clinent function.
updateObject-method | An S4 class to store processed copy number data. (Data processed by using GISTIC2 algorithm)