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The family of R packages containing TCGA data

Data packages submitted to Bioconductor

Installation of packages from the RTCGA family:

Windows users:

Make sure you have rtools installed on your computer.

# packages that are published to devel version of Bioconductor
BiocInstaller::useDevel() # swiches to devel branchof Bioconductor - don't use this line if you are interested in release versions
source("https://bioconductor.org/biocLite.R") # downloads bioClite function
packageinstallationhelpvignettes
RTCGA.rnaseqbiocLite('RTCGA.rnaseq')?rnaseqbrowseVignettes('RTCGA.rnaseq')
RTCGA.clinicalbiocLite('RTCGA.clinical')?clinicalbrowseVignettes('RTCGA.clinical')
RTCGA.mutationsbiocLite('RTCGA.mutations')?mutationsbrowseVignettes('RTCGA.mutations')
RTCGA.mRNAbiocLite('RTCGA.mRNA')?mRNAbrowseVignettes('RTCGA.mRNA')
RTCGA.miRNASeqbiocLite('RTCGA.miRNASeq')?miRNASeqbrowseVignettes('RTCGA.miRNASeq')
RTCGA.PANCAN12biocLite('RTCGA.PANCAN12')?pancan12browseVignettes('RTCGA.PANCAN12')
RTCGA.RPPAbiocLite('RTCGA.RPPA')?RPPAbrowseVignettes('RTCGA.RPPA')
RTCGA.CNVbiocLite('RTCGA.CNV')?CNVbrowseVignettes('RTCGA.CNV')
RTCGA.methylationbiocLite('RTCGA.methylation')?methylationbrowseVignettes('RTCGA.methylation')
# version of packages held at github.com/RTCGA - I try to keep them with the same state as devel versions of Bioconductor
library(RTCGA)
installTCGA("RTCGA.PANCAN12")
installTCGA("RTCGA.CNV")
installTCGA("RTCGA.RPPA")
installTCGA("RTCGA.mRNA")
installTCGA("RTCGA.miRNASeq")
installTCGA("RTCGA.methylation")
# or for all just type installTCGA()

RTCGA

Packages from the RTCGA.data - family/factory are based on the RTCGA package

Installation of the RTCGA package:

To get started, install the latest version of RTCGA from Bioconductor:

BiocInstaller::useDevel() # swiches to devel branch of Bioconductor
source("https://bioconductor.org/biocLite.R") # downloads bioClite function
biocLite("RTCGA") # installs a package

or use below code to download the development version which is like to be less bugged than the release version on Bioconductor:

if (!require(devtools)) {
    install.packages("devtools")
    require(devtools)
}
install_github("RTCGA/RTCGA", build_vignettes = TRUE)

To check Use Cases run

browseVignettes("RTCGA")

Marcin Kosiński, m.p.kosinski@gmail.com

Przemysław Biecek, przemyslaw.biecek@gmail.com

Witold Chodor, witoldchodor@gmail.com

This repository is synchronized with it's Bioconductor's SVN devel mirror.

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Version

Version

1.2.2

License

GPL-2

Maintainer

Marcin Kosinski

Last Published

February 15th, 2017

Functions in RTCGA (1.2.2)

getFirehoseDatasets

Get list of TCGA cohorts.
checkTCGA

Information about datasets from TCGA project
RTCGA-package

The Caner Genome Atlas data integration
FirehoseGISTIC-class

An S4 class to store processed copy number data. (Data processed by using GISTIC2 algorithm)
showResults,DGEResult-method

Export toptable or correlation data frame
getCNGECorrelation

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

An S4 class to store differential gene expression results
getData,FirehoseData-method

Export data from FirehoseData object
convertTCGA

Convert data from RTCGA family to Bioconductor classes
getFirehoseRunningDates

Get standard data running dates.
FirehoseData-class

An S4 class to store main data object from clinent function.
hg19.ucsc.gene.locations

Gene coordinates for circle plot.
datasetsTCGA

RTCGA.data - The Family of R Packages with Data from The Cancer Genome Atlas Study
showResults

Export toptable or correlation data frame
heatmapTCGA

Create Heatmaps for TCGA Datasets
installTCGA

Install packages from RTCGA family
downloadTCGA

Download TCGA data
boxplotTCGA

Create Boxplots for TCGA Datasets
RTCGASample

A sample data object for sample codes.
getDiffExpressedGenes

Perform differential gene expression analysis for mRNA expression data.
kmTCGA

Plot Kaplan-Meier Estimates of Survival Curves for Survival Data
survivalTCGA

Extract Survival Information From RTCGA.clinical Datasets
expressionsTCGA

Gather Expressions for TCGA Datasets
showResults,CorResult-method

Export toptable or correlation data frame
getMutationRate

Make a table for mutation rate of each gene in the cohort
getReport

Draws a circle plot into working directory
infoTCGA

Information about cohorts from TCGA project
getSurvival

Perform survival analysis based on gene expression data
mutationsTCGA

Gather Mutations for TCGA Datasets
pcaTCGA

Plot Two Main Components of Principal Component Analysis
CorResult-class

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

Get data from Firehose portal.
FirehosemRNAArray-class

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

Read TCGA data to the tidy format
FirehoseCGHArray-class

An S4 class to store data from CGA platforms
getData

Export data from FirehoseData object
theme_RTCGA

RTCGA Theme For ggplot2
FirehoseMethylationArray-class

An S4 class to store data from methylation platforms
RTCGAToolbox

RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
getFirehoseAnalyzeDates

Get data analyze dates.