Example re-analysis of an Influenza Vaccine Response Study using HAI (hemagglutination inhibition) assays
In this tutorial we will show you how to acquire, analyze, and display the demographic and HAI assay data from one study in ImmPort using R and Python analysis code. The code is freely available.
The demographic data can be graphically rendered to facilitate exploration of age, gender and population characteristics of the study subjects.
HAI results can be grouped by titer pre- and post-vaccination in a single overview plot.
HAI results can be displayed according to subject age and viral strain.
There are two versions of the analysis code, one written in R and the other in Python. Both versions complete the same analysis steps and render graphic summaries of the results.
Analysis using R
The analysis code was developed to use either the MySQL or the Tab version of the data.
The details of the code that uses the MySQL data format and the graphics it produces are available
An example HTML output from running the Tab version of the code is available
The R code for running the analysis using the MySQL version is available for download
The R Markdown code for running the analysis using the MySQL version is available for download
The R code for running the analysis using the Tab version is available for download
The R Markdown code for running the analysis using the Tab version is available for download
The code was written using RMarkdown and was developed and executed using the