This package provides a GUI overlay for the MSGFplus package, and by extension the MS-GF+ algorithm for peptide identification in LC-MS/MS data files. Most functionality of the app is hidden behind the function MSGFgui which summons the GUI in your browser of choice. Do note that MSGFgui relies on a modern browser that supports HTML5, CSS3 and SVG. This means that people trapped in Internet Explorer 8 and below will probably have trouble getting this to work - but then again they certainly have other things to worry about. Please consult the vignette for a run-through of the functionality exposed in the GUI.
MSGFgui
(Package: MSGFgui) :
Start MSGFgui in the default browser
This function load the GUI in the users default browser. Due to some unfortunate problems with shiny, the user needs to refresh the webpage the first time it loads in order for everything to work properly. This will likely be fixed in a coming shiny release. For the time being MSGFgui is designed to run locally. This means that there is automatic view rights to the full file system of the computer running the server.
currentData
(Package: MSGFgui) :
Gets the result data currently in use by another R session running MSGFgui
This function makes it possible to directly access the data used in the gui by starting a new R session and running this function. This will only work if just one instance of MSGFgui is running in the browser. The data will linger on so calling currentData() when no instance of MSGFgui is running will return the last set of data used.
providing 
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