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.
MSGFgui and it's sister package MSGFplus are part of Bioconductor and can be installed through that repository. Instruction are as follows:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install('MSGFplus')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.