README.md

In GeneSurvey/TCGAGeneReport: Access to Gene Report Data

This repository has been superseded.

Please use the following repositories.

https://github.com/MD-Anderson-Bioinformatics/GeneSurvey

https://github.com/MD-Anderson-Bioinformatics/ReadMatrixRcpp

https://github.com/MD-Anderson-Bioinformatics/GSAccess

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BELOW IS SUPERSEDED

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TCGAGeneReport

This is for educational and research purposes only.

http://bioinformatics.mdanderson.org

The goal of the Gene Survey project is to take TCGA Standardized Data and make gene level cross-disease and sometimes cross platform comparisons and evaluations simpler to perform, as these represent common questions asked of researchers and analysts. That is, we are answering a common question: how does gene XYZ act across disease types?

This is the R package used for this project. The Java package is available at https://github.com/GeneSurvey/TcgaGSData but the JAR is included with this source.

The data file will be available soon.

General Prerequisites

The TCGAGeneReport package requires Java 1.8.

These instructions have been tested using R 3.2.3 and R 3.2.2.

Linux Prerequisites

Linux (Debian/Ubuntu) install the Linux DEB packages: libssl-dev, libxml2-dev, libcurl4-openssl-dev, lzma, lzma-dev, and liblzma-dev.

Other distributions will have similar packages. The devtools install will indicate what Linux installs are missing.

As the user with sudo access and which will run RStudio, set the JAVA_HOME variable. (This is the directory above the bin, for example, the javac at /usr/local/jdk1.8.0_45/bin/javac should be entered as /usr/local/jdk1.8.0_45.)

Windows Prerequisites

Do a javareconf for R using "R CMD javareconf". Make sure Java 1.8 is registered with R.

Windows installations will also need any extras needed for compiling R packages.

R Prerequisites

The devtools and rJava package need to be installed.

install.packages("devtools", dependencies=TRUE)
install.packages("rJava", dependencies=TRUE)

Linux Install

devtools::install_github("GeneSurvey/TCGAGeneReport")

Windows Install

If you are setup for multi-architecture compiles in Windows, you can remove the args parameter.

devtools::install_github("GeneSurvey/TCGAGeneReport", args="--no-multiarch")

Useful Tests

This can be used to test your rJava install and Java version.

library(rJava)
.jinit()
J("java.lang.System")$getProperty("java.version")

Other Projects

The TcgaIdConverter and TcgaGSData Java projects are used by this R package. For installing TCGAGeneReport, you do not need to do anything with those projects on GitHub. This R package already has copies of those projects' JAR files.

GeneSurvey/TCGAGeneReport documentation built on May 6, 2019, 6:27 p.m.