Approaches to Assay Processing Package Validation

rstudio::conf 2020 pharma

Ellis Hughes

January 30, 2020

In this talk I will discuss the steps that have been created for validating internally generated R packages at SCHARP (Statistical Center for HIV/AIDS Research and Prevention) and the lessons learned while creating packages as a team. Housed within Fred Hutch, SCHARP is an instrumental partner in the research and clinical trials surrounding HIV prevention and vaccine development. Part of SCHARP’s work involves analyzing experimental biomarkers and endpoints which change as the experimental question, analysis methods, antigens measured, and assays evolve. Maintaining a validated code base that is rigid in its output format, but flexible enough to cater a variety of inputs with minimal custom coding has proven to be important for reproducibility and scalability. SCHARP has developed several key steps in the creation, validation, and documentation of R packages that take advantage of R’s packaging functionality. First, the programming team works with leadership to define specifications and lay out a roadmap of the package at the functional level. Next, statistical programmers work together to develop the package, taking advantage of the rich R ecosystem of packages for development such as roxygen2, devtools, usethis, and testthat. Once the code has been developed, the package is validated to ensure it passes all specifications using a combination of testthat and rmarkdown. Finally, the package is made available for use across the team on live data. These procedures set up a framework for validating assay processing packages that furthers the ability of Fred Hutch to provide world-class support for our clinical trials.

About the speaker

Ellis Hughes

I am a statistical Programmer at Fred Hutch Cancer Research Center where I work on a team that evaluates potential HIV vaccine candidates. Having graduated from Washington State University with a degree in Bioengineering, I found a passion for programming in R. I now organize the Seattle UseR group, and enjoy building packages to automate my workflows.