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Working with Cancer Genomics Browser data in R / Bioconductor
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vignettes
CGBTutorial.pdf
DESCRIPTION
LICENSE
NAMESPACE
README.md

README.md

CGBTutorial

This tutorial illustrates how files obtained from the Cancer Genomics Browser (CGB) can be loaded into appropriate R / Bioconductor data structures, and how data can be handled to arrive at results comparable to those in CGB demos.

The CGBTutorial vignette can be used as a stand-alone reference.

Package Installation

Two functions to help with data import are provide in this package. To use these, the package requires at least the 2.4 branch of Bioconductor. This is the devel branch on 6 November, 2013.

  1. Export this repository github.
  2. Install the package dependencies

    source("http://bioconductor.org/biocLite.R")
    biocLite("Biobase")
    
  3. Download TCGA_BRCA_G4502A_07_3-2013-10-29.tgz and TCGA_BRCA_GSNP6noCNV-2013-10-29.tgz from the CGB, and place this in the CGBTutorial/inst/bigdata directory

  4. Build and install the package

    R CMD build CGBTutorial
    R CMD INSTALL CGBTutorial_0.0.2.tar.gz
    
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