Topic outline

  • Statistical methods for big data in life sciences and health with R

    Lausanne, 3-6 June 2019

    University of Lausanne, room 202 - Amphipôle building

    This page is addressed to registered participants. To access course description and application form, please click here.

    For any assistance, please contact training@sib.swiss.


  • Schedule

    Subject to changes

    Day 1.

    • Overview: big data case studies in health domain
    • Identify the general challenges behind big data analysis (model and overfitting)
    • Big data visualisation

    Day 2. 

    • RevoScaleR 
    • Linear models

    Day 3.

    • Big data exploration and classifications
    • Machine learning and decisional algorithms – unsupervised learning

    Day 4.

    • Introduction to: Decision Tree, Random forest, Neural Networks, Deep learning

    • Installation prior to course

      You are required to bring your own laptop, with a working Wifi connection, and the latest versions of R and RStudio installed.

      For this course you have to download data sets, confirgure Rstudio and install a virtual machine.


      STEP1
      From the following URL, download the file ZIP file, unzip it, you should end up with a XPT file.


      STEP2
      If not yet done, please also install the following packages by executing in R studio the following commands:

      install.packages("epitools")
      install.packages("taRifx")
      install.packages("data.table")
      install.packages("reshape")
      install.packages("dplyr")
      install.packages("plyr")
      install.packages("utils")
      install.packages("microbenchmark")


      install.packages("rpart")
      install.packages("rpart.plot")
      install.packages("randomForest")
      install.packages("ggplot2")

      install.packages("devtools")
      devtools::install_github("rstudio/keras")
      library(keras)
      install_keras()
      install.packages("ggfortify”)


      STEP3
      Prior to the course, you will need to have an emulation of a Linux OS, i.e. a virtual machine containing among others a terminal window. This will be used for the practicals.

      REQUIREMENTS: you need a computer with minimum of 4 GB memory. The virtual machine itself requires 4 GB memory. And at least 25 GB free space on your hard disk.

      To this end, you first need to have Virtualbox installed on your computer. Please download and install the (latest) version of VirtualBox according to your operating system (Windows or Mac, no need for Unix/Linux machines). 
      https://www.virtualbox.org/wiki/Downloads


      Then download the virtual machine image (.ova) here on your computer. 

      To install and run it, please read the Virtual Machine installation guide.
      If at the end of the procedure, you are not able to run the virtual machine, please contact us sufficiently in advance at training@sib.swiss as no technical problem with the virtual machine will be handled during the course. Mac users can work with their terminal and for Windows users, we will propose you an alternative with a terminal app install (MobaXterm).

      For the practicals, please follow the different steps explained in the guide (see pdf document below).