TCGA

Welcome to my analysis project of The Cancer Genome Atlas{target="_blank"}!

This little project makes use of ProjectTemplate{target="_blank"} in order to automate the boring stuff of any project:

• it creates the directory structure and populates it with some information on what to do with each directory
• it manages all your needed packages in a central location config/global.dcf
• it can load and preprocess your data, enabling you to start with the important stuff - the analyses
• you can cache intermediate files or big data structures to minimize reload times

Following some contents of the README.md which would be created by ProjectTemplate:

ProjectTemplate is an R package that helps you organize your statistical analysis projects. Since you're reading this file, we'll assume that you've already called create.project() to set up this project and all of its contents. To load your new project, you'll first need to setwd() into the directory where this README file is located. Then you need to run the following two lines of R code:

	library('ProjectTemplate')
	load.project()

After you enter the second line of code, you'll see a series of automated messages as ProjectTemplate goes about doing its work. This work involves:

• Reading in the global configuration file contained in config.
• Loading any R packages you listed in the configuration file.
• Reading in any datasets stored in data or cache.
• Preprocessing your data using the files in the munge directory.
  Once that's done, you can execute any code you'd like. For every analysis you create, we'd recommend putting a separate file in the src directory. If the files start with the two lines mentioned above:

	library('ProjectTemplate')
	load.project()

You'll have access to all of your data, already fully preprocessed, and all of the libraries you want to use. For more details about ProjectTemplate, see http://projecttemplate.net