Man pages for mksamur/RTCGAToolbox
A new tool for exporting TCGA Firehose data

biocExtractExtract and convert data from a 'FirehoseData' object to a...
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.)...
getBroadSubtypesDownload expression-based cancer subtypes from the Broad...
getCNGECorrelationPerform correlation analysis betwwen gene expression and copy...
getDataExtract 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.
getGISTICPeaksDownload GISTIC2 peak-level data from the Firehose pipeline
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
selectTypeAccessor function for the FirehoseData object
showResultsExport toptable or correlation data frame
showResults-CorResultExport toptable or correlation data frame
showResults-DGEResultExport toptable or correlation data frame
mksamur/RTCGAToolbox documentation built on Feb. 6, 2018, 2:06 p.m.