I'm writing an R package I intend to submit to Bioconductor. The aim of the package is to analyse high throughput proteomics data, starting from the MaxQuant evidence file. I feel it is necessary to show step-by-step examples of such analysis in a vignette. However, this would require attaching large files, tens of MB each to the package.
What is the best practice in such cases?
I could reduce the size by selecting a small sample of random rows from the actual evidence data, but this would reduce numbers of peptides and proteins and the statistical power drastically, making the example unrealistic.
Alternatively, I could create a separate package containing only example data. The vignette of the original package would request the data package and demonstrate how to process real data.