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 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 |
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) |