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Fri 6 Jul 2018
09:30 - 17:00

Venue: Bioinformatics Training Room, Craik-Marshall Building

Provided by: Bioinformatics


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R object-oriented programming and package development

Fri 6 Jul 2018


The course will teach intermediate R object-oriented programming and how to build a fully functional R package.

Relevant teaching materials are available here and the sequences example package used as template in the course can be found here.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
  • A good knowledge of R and some active programming experience is required.
  • Only attending Introduction to R would not provide sufficient background for this course.
  • Familiarity with object-oriented programming would be an advantage, but is not essential.

Number of sessions: 1

# Date Time Venue Trainers
1 Fri 6 Jul 2018   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building map Robert Stojnic,  Laurent Gatto
Topics covered

Bioinformatics, Software engineering


After this course you should be able to:

  • use object-oriented programming in R and build your own packages

During this course you will learn about:

  • What is object-oriented programming; description of the working example; R programming best practices: tips and tricks, environments, coding standards
  • R object-oriented programming: the S3 and S4 OO systems
  • Documentation: documenting functions, methods and data, providing executable examples; documentation using Roxygen; executing R
  • Writing R packages: minimum package structure; combining the written classes/generics/methods and documentation to create a package; building, checking and installing packages
  • Other advanced R programming topics: testing code, unit testing; profiling and debugging; calling C code inside R

Presentations, demonstrations, and exercises


Time Topics
9:30 - 10:00 R package basics
10:00 - 11:00 Object-oriented programming part I
11:00 - 11:15 Tea/Coffee Break
11:15 - 12:30 Object-oriented programming part II
12:30 - 13:30 Lunch (not provided)
13:30 - 15:00 Package commands and structure; writing R documentation
15:00 - 15:15 Tea/Coffee Break
15:15 - 17:00 Package unit testing; distributing packages
Registration Fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here



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