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 established Bioconductor classes:
Identification results are parsed and imported as
PSMatch::PSM() objects with sagePSM().
Quantitation (and identification) results are parsed, merged and
imported as QFeatures::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.
Sage: proteomics searching so fast it seems like magic. https://github.com/lazear/sage.
Yu et al. 'Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics' Anal. Chem. 2020, 92, 9, 6478–6485 Publication Date:April 6, 2020 DOI:10.1021/acs.analchem.9b05685.
Useful links:
Report bugs at https://github.com/UCLouvain-CBIO/sager/issues