sager: Analysing sage results with R

The sager package can be used to import results produced by the sage search engine into R. Sage produces tab-separated output files for identification and quantitation results. In sager, we import these result files into establised Bioconductor classes:

• Identification results are parsed and imported as PSM objects with sagePSM().

• Quantitation (and identification) results are parsed, merged and imported as QFeatures objects with sageQFeatures().

These functions are described and demonstrated in their respective manual pages using data generated from Yu et al. Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics, downloaded from ProteomeXchange project PXD016766. See sagerData() for details.

If you want to install and try the package out:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("UCLouvain-CBIO/sager")

If you run into issues of have questions, please open an issue.