A new tool for exporting TCGA Firehose data

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Documentation for package ‘RTCGAToolbox’ version 2.34.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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
getData	Extract data from FirehoseData object
getData-method	An S4 class to store main data object from clinent function.
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.
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)