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
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
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.
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