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Tutorial Setup

Setup

For the following machine learning tutorials we will be using glioblastoma data from cBioPortal. When working within R it is useful to set up an R project. R projects will set your working directory relative to the project directory. This can help ensure you are only working with files within this project space. To create a new project:

  1. Go to File > New Project
  2. New Directory
  3. New Project
  4. Create a name for your project (e.g. machine_learning)
  5. Create Project

When analyzing data it is useful to create a folder to house your raw data, scripts and results. We can do this by clicking the New Folder icon to create these folders:

  1. Click New Folder > Enter data > Click OK
  2. Click New Folder > Enter scripts > Click OK
  3. Click New Folder > Enter results > Click OK

Now that we have our project set up we will need to download our data. In the data folder we will download our data and decompress it:

download.file(url = "https://cbioportal-datahub.s3.amazonaws.com/gbm_cptac_2021.tar.gz",destfile = "./data/gbm_cptac_2021.tar.gz" )
untar(tarfile = "./data/gbm_cptac_2021.tar.gz",exdir = "./data/")