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R Programming II logo

Purpose: To test your fundamental R package development skills.

Pre-requisites: Required: R Programming I

Instructions

The following instructions describe the requirements to complete this task and earn the R Programming II badge 🏆. They also provide guidance to help you along the way.

A few things to keep in mind:

  1. Please remember at all times to abide by the BRN Code of Conduct and Academic Honesty Policy. If you notice violations of these policies, please contact codeofconduct@bioresnet.org.
  2. Please remember to reach out if you get stuck, find bugs, or even just have a question!

Good luck and have fun! 😊

~ BRN Bot 🤖

Requirements

Badge Requirements:

Testing environment:

Assessment Premise:

TLDR; Take the functions from R Programming I and turn them into a package called "BioUtils"

After you completed the tasks your supervisor gave you in R Programming I, you get a call from HR. Apparently, your functions were so useful that you have been promoted from a Bioinformatics Assistant to Bioinformatics Associate 🚀. Your first task will be to turn your utils.R script into a package, BioUtils, for the whole bioinformatics team to use 🎯. The package should contain all the functions you wrote in utils.R, but properly formatted as an R package and well-documented. This will enable your colleagues to easily install your package and use the functions contained within!

Users will use your package like so:

library(BioUtils)

cancer <- "ATCGCATACGA"
normal <- "ATCCCAGATGA"

protein_variant(cancer, normal)

Automated testing / checking

Prior to releasing the package, your new supervisor will make sure that everything works correctly and that it is well-formatted/documented. She will deploy a bot to run automated checks on your package -- they should produce no errors, warnings, or notes.

Automated checks

The bot will initiate an R v4.2.0 session and install BioUtils package by running:

devtools::build()

Then it will test the package by running:

devtools::test()

Next, it will run CRAN checks:

devtools::check(cran = TRUE, error_on="note")

Next, it will check the style of the package using lintr from the linux command line:

Rscript -e "errors <- lintr::lint_package(); print(errors); quit(save = 'no', status = length(errors))"

Guidance

Most guidance for this assessment is identical to R Programming I, with the following additions:

Due to naming conventions in R packages, it is a very good idea to clone this github repository with the name BioUtils specified for the output directory:

git clone <link_to_repo> BioUtils

Additional resources

To learn about building and documenting R packages, visit the following link: R packages book

The easiest way to complete this assignment is to make heavy usage of the usethis R package: link. For example, it is strongly recommended to begin this task by running usethis::create_package(). When adding new datasets to the package, it is recommended to run usethis::use_data_raw() to initialize them.

Getting help

If you find a bug or get confused, please don't hesitate to contact the BRN Skill Assessment maintainers on the #help-skill-assessments Slack channel, and they will assist you.