README.md

In thomasp85/MSGFplus-release: 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 as well as a very simple gWidgets based GUI to fill out a msgfPar object.

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 and it's sister package MSGFplus is intented for inclusion within the next Bioconductor release. Until then, try it out by installing as follows:

source("http://bioconductor.org/biocLite.R")
biocLite('mzR')
biocLite('mzID')
install.packages('shiny')
install.packages('devtools')
install_github('MSGFplus', 'thomasp85')

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-release documentation built on May 31, 2019, 11:09 a.m.