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Version

Version

2.2.2

License

GPL (>= 2)

Maintainer

Mehmet Kemal Samur

Last Published

February 15th, 2017

Functions in RTCGAToolbox (2.2.2)

getSurvival

Perform survival analysis based on gene expression data
FirehoseData-class

An S4 class to store main data object from clinent function.
getData

Export data from FirehoseData object
showResults,CorResult-method

Export toptable or correlation data frame
getFirehoseAnalyzeDates

Get data analyze dates.
getFirehoseDatasets

Get list of TCGA cohorts.
getData,FirehoseData-method

Export data from FirehoseData object
showResults,DGEResult-method

Export toptable or correlation data frame
DGEResult-class

An S4 class to store differential gene expression results
RTCGAToolbox

RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
getDiffExpressedGenes

Perform differential gene expression analysis for mRNA expression data.
FirehosemRNAArray-class

An S4 class to store data from array (mRNA, miRNA etc.) platforms
RTCGASample

A sample data object for sample codes.
getFirehoseRunningDates

Get standard data running dates.
CorResult-class

An S4 class to store correlations between gene expression level and copy number data
showResults

Export toptable or correlation data frame
hg19.ucsc.gene.locations

Gene coordinates for circle plot.
getCNGECorrelation

Perform correlation analysis betwwen gene expression and copy number data
FirehoseCGHArray-class

An S4 class to store data from CGA platforms
getMutationRate

Make a table for mutation rate of each gene in the cohort
FirehoseGISTIC-class

An S4 class to store processed copy number data. (Data processed by using GISTIC2 algorithm)
getReport

Draws a circle plot into working directory
getFirehoseData

Get data from Firehose portal.
FirehoseMethylationArray-class

An S4 class to store data from methylation platforms