CRG Introduction to R 2018

From Bioinformatics Core Wiki

Description

This is an introductory course to R programming.
The course is offered in 4 slow-paced practicums for absolute beginners. The goal is to offer a good base with a lot of hands on exercises.
We will use the R Studio of the CRG server.

Course Instructor

  • Sarah Bonnin - Bioinformatician at the CRG bioinformatics core facility.


Dates, Time and Location

  • March 19-20 & April 16-17
  • 10:00 - 14:00
  • PRBB Bioinformatics classroom (468). 4th floor. The hotel/North wing.


Course Syllabus, Schedule, and Materials

The day before each session, the slides will be uploaded in case you want to print them.

  • Day 1
    • Introduction to R Studio
      We will use the R Studio of the CRG server (http://rstudio.linux.crg.es). We will go through what can be done with R Studio, from file and folder manipulation/navigation, to getting help on R functions.
    • Paths / directories
    • Basics of R: syntax, create an object, manipulate the object, simple arithmetics.
    • Functions usage in R
      Arguments. Get help.
    • R scripts: write and save commands, run them as a block. Comment code.
    • Data types.
    • Data structures:
      • Vectors
        Basic (and most important) data structure in R. We will learn how to create, modify, subset, manipulate, compare vectors.
      • Introduction to factors: categorical vectors.

Slides day1
Exercises day 1 (1, 2 & 3)
Correction of exercises:



  • Day 2
    • Missing values: how to deal with NA values.
    • Matrices & data frames
      2-dimensional objects: how to create, subset, select, manipulate.

Slides day2
Exercises day 2 (4 & 5)
Correction of exercises:


  • Day 3
    • Input / output
      Reading in and writing out files. Adapting I/O to file format.
    • Library / packages
      Install and load packages. Look for functions in those packages.

Slides day3
Exercises day 3 (6 & 7)
Correction of exercises:


  • Day 4
    • Basic plotting (base graphics package)
      Scatter plots, boxplots, barplots, pie plots, histograms.
    • Introduction to ggplot2 package
      ggplot2 provides functions for creating and customizing plots. We will learn the basic structure and how to produce simple plots.
    • Input / output
      We will save plots as files in different formats, both from R Studio and from the terminal.

Slides day4
Exercises day 4 (8 & 9)
Correction of exercises:

Resources

Bioinformatics Core Facility @ CRG — 2011-2018