Sample analysis

We are having monthly sessions to explore R and DataSHIELD and share experiences. Each month a cohort is leading the session and explaining R functionality in a script they produce. We have created the following guidelines to share our experiences in code with each other.

Repository structure

When you run a workshop in the R-group you should post your script files into the following directory structure.

• sample_analysis
  • NINFEA
    • sample_analysis_ninfea.R
  • SWS
    • sample_analysis_sws.R
  • DNBC
    • sample_analysis_dnbc.R
  • etc.

This way we can maintain a single source of sample analysis and work on a shared knowledge base.

note: In the sample analysis directory you can work on the same file, but it is not recommended.

Tools for doing sample analysis

We have now defined a toolset to do the sample analysis.

• dsBetaTest library of DataSHIELD
• gcipdr package of https://github.com/bonorico

Testing new DataSHIELD functionality with dsBetaTest

To test new functionality we have created a development environment which can be found here:

• https://cohort-opal2.test.molgenis.org
• https://analysis.test.molgenis.org (RStudio with DataSHIELD)

Generating data with gcipdr

Check https://github.com/bonorico