A new tool for exporting TCGA Firehose data

[Up] [Top]

Documentation for package ‘RTCGAToolbox’ version 2.10.0

Help Pages

RTCGAToolbox-package RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
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 betwwen 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
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.
RTCGASample A sample data object for sample codes.
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)