We will generally follow the conventions described in R Packages by Hadley Wickham. JoesFlow is set up using the same conventions we will be using here.
- R: R code (i.e. functions)
- inst/extdata: Raw data files that are not generated by the package itself
- shiny: Final Shiny app code (i.e. not for Shiny components, they will reside in
R/, but for the app that will be installed on the Shiny server) - tests: Unit testing code
- docs: This is where web documentation (i.e. vignettes) will be generated when we get to that part.
Other directories (i.e. man) will be auto-generated during package compilation.
We will use roxygen2 tags for documentation.
...put data documentation here for now
Description: The test data were sourced from the PRIDE Archive, specifically from the project PXD038652(PRIDE Archive Project). The dataset includes proteocims data on cow proteins (Bos taurus), which were analyzed to identify and quantify the protein groups present.
PRIDE Archive. (2023). "PXD038652: Proteomics data on Bos taurus proteins." European Bioinformatics Institute (EBI). Available at: https://www.ebi.ac.uk/pride/archive/projects/PXD038652.
Publication List Serafim TD, Iniguez E, Barletta ABF, Cecilio P, Doehl JSP, Short M, Lack J, Nair V, Disotuar M, Wilson T, Coutinho-Abreu IV, Meneses C, Andersen J, Alves E Silva TL, Oliveira F, Vega-Rodriguez J, Barillas-Mury C, Ribeiro JMC, Beverley SM, Kamhawi S, Valenzuela JG, Leishmania genetic exchange is mediated by IgM natural antibodies. Nature, 623(7985):149-156(2023) https://www.ncbi.nlm.nih.gov/pubmed?term=37880367
We will use devtools to help with package building. The following commands will be used:
# documentation generation / updates
devtools::document()
# package checking
devtools::check()
# package testing (also run as part of `check`, but if you only want to run tests)
devtools::test()
# package installation
devtools::install()
# Once the package is ready, you can start the Shiny app with:
ProtResDash::run_app()