Man pages for Bioconductor-mirror/RTCGAToolbox
A new tool for exporting TCGA Firehose data

CorResult-classAn S4 class to store correlations between gene expression...
DGEResult-classAn S4 class to store differential gene expression results
FirehoseCGHArray-classAn S4 class to store data from CGA platforms
FirehoseData-classAn S4 class to store main data object from clinent function.
FirehoseGISTIC-classAn S4 class to store processed copy number data. (Data...
FirehoseMethylationArray-classAn S4 class to store data from methylation platforms
FirehosemRNAArray-classAn S4 class to store data from array (mRNA, miRNA etc.)...
getCNGECorrelationPerform correlation analysis betwwen gene expression and copy...
getDataExport data from FirehoseData object
getData-methodsExport data from FirehoseData object
getDiffExpressedGenesPerform differential gene expression analysis for mRNA...
getFirehoseAnalyzeDatesGet data analyze dates.
getFirehoseDataGet data from Firehose portal.
getFirehoseDatasetsGet list of TCGA cohorts.
getFirehoseRunningDatesGet standard data running dates.
getMutationRateMake a table for mutation rate of each gene in the cohort
getReportDraws a circle plot into working directory
getSurvivalPerform survival analysis based on gene expression data
hg19.ucsc.gene.locationsGene coordinates for circle plot.
RTCGASampleA sample data object for sample codes.
RTCGAToolboxRTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
showResultsExport toptable or correlation data frame
showResults-CorResultExport toptable or correlation data frame
showResults-DGEResultExport toptable or correlation data frame
Bioconductor-mirror/RTCGAToolbox documentation built on May 31, 2017, 11:39 p.m.