README.md

In thomasp85/MSGFplus: An interface between R and MS-GF+

MSGFplus

This package aims to bridge R and the peptide database search tool MS-GF+. The main class of the package is msgfPar which handles parsing of parameters to MS-GF+. The msgfPar class has a runMSGF method that starts a peptide search for a given set of MS data files and possibly reimports the results using mzID.

Besides this basic functionality it also supports reading in parameters from mzIdentML files created by MS-GF+ in order to replicate a search setup.

MSGFplus is intended as a pure R wrapper. For a more engaging user experience have a look at MSGFgui which provides a visual interface on top of this package using shiny.

Installation

MSGFgui was in Bioconductor until version 3.14. It as been removed but is still available on Github, although not actively maintained anymore.

remotes::install_github('thomasp85/MSGFplus')

Credit

Sangtae Kim is the developer behind the MS-GF+ algoritm, without which this package would be rather shallow. Furthermore he has provided fast and helpful feedback during the development process.

References

1. MSGFgui (R based GUI for MSGFplus)
2. MS-GF+ (Original Java program)
3. mzID (R package)

thomasp85/MSGFplus documentation built on Oct. 2, 2024, 9:26 a.m.