This github project has an accompanying website created with pkgdown. https://prolfqua.github.io/prolfquabenchmark/

prolfquaBenchmark - Benchmarking LFQ data analysis using the prolfqua package.

The R package prolfquabenchmark contains vignettes which show how we used the IonStar dataset to asses the performance of the methods implemented in the prolfqua R packages and other packages (MSstats, proDA).

• Benchmarking FragPipe output using Ionstar Dataset
• Benchmarking MSstats using the Ionstar Dataset
• Benchmarking the proDA package using the Ionstar Dataset MQ LFQ intensities
• Benchmarking the proDA package using the Ionstar Dataset starting from peptides
• Benchmarking normalization, aggregation and models using the Ionstar Dataset

How to install and generate the vignettes

Download the latest prolfqua release from from https://github.com/fgcz/prolfqua/releases And then install it by running on the command:

R CMD INSTALL prolfqua_X.Y.Z.tar.gz

Or in the R session:

install.packages("prolfqua_X.Y.Z.tar.gz",repos = NULL, type="source")

Afterwards you also will need to install the prolfquadata package

install.packages('remotes')
remotes::install_gitlab("wolski/prolfquadata", host="gitlab.bfabric.org")

Finally you can clone the repository and open it in RStudio and build the vignettes with

devtools::build_vignettes()

Or build them on the command line by running

R CMD build prolfquaBenchmark