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RTCGAToolbox
Please visit
http://mksamur.github.io/RTCGAToolbox/
or check vignette for more details!
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Version
Version
2.2.2
2.0.0
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Version
2.2.2
License
GPL (>= 2)
Maintainer
Mehmet Kemal Samur
Last Published
May 28th, 2015
Functions in RTCGAToolbox (2.2.2)
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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